Fast and accurate quantum molecular dynamics of dense plasmas across temperature regimes
Sjostrom, Travis; Daligault, Jerome
2014-10-10
Here, we develop and implement a new quantum molecular dynamics approximation that allows fast and accurate simulations of dense plasmas from cold to hot conditions. The method is based on a carefully designed orbital-free implementation of density functional theory. The results for hydrogen and aluminum are in very good agreement with Kohn-Sham (orbital-based) density functional theory and path integral Monte Carlo calculations for microscopic features such as the electron density as well as the equation of state. The present approach does not scale with temperature and hence extends to higher temperatures than is accessible in the Kohn-Sham method and lowermore » temperatures than is accessible by path integral Monte Carlo calculations, while being significantly less computationally expensive than either of those two methods.« less
Fast and accurate quantum molecular dynamics of dense plasmas across temperature regimes
Sjostrom, Travis; Daligault, Jerome
2014-10-10
Here, we develop and implement a new quantum molecular dynamics approximation that allows fast and accurate simulations of dense plasmas from cold to hot conditions. The method is based on a carefully designed orbital-free implementation of density functional theory. The results for hydrogen and aluminum are in very good agreement with Kohn-Sham (orbital-based) density functional theory and path integral Monte Carlo calculations for microscopic features such as the electron density as well as the equation of state. The present approach does not scale with temperature and hence extends to higher temperatures than is accessible in the Kohn-Sham method and lower temperatures than is accessible by path integral Monte Carlo calculations, while being significantly less computationally expensive than either of those two methods.
Surface electron density models for accurate ab initio molecular dynamics with electronic friction
NASA Astrophysics Data System (ADS)
Novko, D.; Blanco-Rey, M.; Alducin, M.; Juaristi, J. I.
2016-06-01
Ab initio molecular dynamics with electronic friction (AIMDEF) is a valuable methodology to study the interaction of atomic particles with metal surfaces. This method, in which the effect of low-energy electron-hole (e-h) pair excitations is treated within the local density friction approximation (LDFA) [Juaristi et al., Phys. Rev. Lett. 100, 116102 (2008), 10.1103/PhysRevLett.100.116102], can provide an accurate description of both e-h pair and phonon excitations. In practice, its applicability becomes a complicated task in those situations of substantial surface atoms displacements because the LDFA requires the knowledge at each integration step of the bare surface electron density. In this work, we propose three different methods of calculating on-the-fly the electron density of the distorted surface and we discuss their suitability under typical surface distortions. The investigated methods are used in AIMDEF simulations for three illustrative adsorption cases, namely, dissociated H2 on Pd(100), N on Ag(111), and N2 on Fe(110). Our AIMDEF calculations performed with the three approaches highlight the importance of going beyond the frozen surface density to accurately describe the energy released into e-h pair excitations in case of large surface atom displacements.
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.
Ganesh, P; Jiang, De-en; Kent, P R C
2011-03-31
Lithium-ion batteries have the potential to revolutionize the transportation industry, as they did for wireless communication. A judicious choice of the liquid electrolytes used in these systems is required to achieve a good balance among high-energy storage, long cycle life and stability, and fast charging. Ethylene-carbonate (EC) and propylene-carbonate (PC) are popular electrolytes. However, to date, almost all molecular-dynamics simulations of these fluids rely on classical force fields, while a complete description of the functionality of Li-ion batteries will eventually require quantum mechanics. We perform accurate ab initio molecular-dynamics simulations of ethylene- and propylene-carbonate with LiPF(6) at experimental concentrations to build solvation models which explain available neutron scattering and nuclear magnetic resonance (NMR) results and to compute Li-ion solvation energies and diffusion constants. Our results suggest some similarities between the two liquids as well as some important differences. Simulations also provide useful insights into formation of solid-electrolyte interphases in the presence of electrodes in conventional Li-ion batteries.
Schwörer, Magnus; Lorenzen, Konstantin; Mathias, Gerald; Tavan, Paul
2015-03-14
Recently, a novel approach to hybrid quantum mechanics/molecular mechanics (QM/MM) molecular dynamics (MD) simulations has been suggested [Schwörer et al., J. Chem. Phys. 138, 244103 (2013)]. Here, the forces acting on the atoms are calculated by grid-based density functional theory (DFT) for a solute molecule and by a polarizable molecular mechanics (PMM) force field for a large solvent environment composed of several 10(3)-10(5) molecules as negative gradients of a DFT/PMM hybrid Hamiltonian. The electrostatic interactions are efficiently described by a hierarchical fast multipole method (FMM). Adopting recent progress of this FMM technique [Lorenzen et al., J. Chem. Theory Comput. 10, 3244 (2014)], which particularly entails a strictly linear scaling of the computational effort with the system size, and adapting this revised FMM approach to the computation of the interactions between the DFT and PMM fragments of a simulation system, here, we show how one can further enhance the efficiency and accuracy of such DFT/PMM-MD simulations. The resulting gain of total performance, as measured for alanine dipeptide (DFT) embedded in water (PMM) by the product of the gains in efficiency and accuracy, amounts to about one order of magnitude. We also demonstrate that the jointly parallelized implementation of the DFT and PMM-MD parts of the computation enables the efficient use of high-performance computing systems. The associated software is available online. PMID:25770527
Schwörer, Magnus; Lorenzen, Konstantin; Mathias, Gerald; Tavan, Paul
2015-03-14
Recently, a novel approach to hybrid quantum mechanics/molecular mechanics (QM/MM) molecular dynamics (MD) simulations has been suggested [Schwörer et al., J. Chem. Phys. 138, 244103 (2013)]. Here, the forces acting on the atoms are calculated by grid-based density functional theory (DFT) for a solute molecule and by a polarizable molecular mechanics (PMM) force field for a large solvent environment composed of several 10{sup 3}-10{sup 5} molecules as negative gradients of a DFT/PMM hybrid Hamiltonian. The electrostatic interactions are efficiently described by a hierarchical fast multipole method (FMM). Adopting recent progress of this FMM technique [Lorenzen et al., J. Chem. Theory Comput. 10, 3244 (2014)], which particularly entails a strictly linear scaling of the computational effort with the system size, and adapting this revised FMM approach to the computation of the interactions between the DFT and PMM fragments of a simulation system, here, we show how one can further enhance the efficiency and accuracy of such DFT/PMM-MD simulations. The resulting gain of total performance, as measured for alanine dipeptide (DFT) embedded in water (PMM) by the product of the gains in efficiency and accuracy, amounts to about one order of magnitude. We also demonstrate that the jointly parallelized implementation of the DFT and PMM-MD parts of the computation enables the efficient use of high-performance computing systems. The associated software is available online.
A simple and accurate algorithm for path integral molecular dynamics with the Langevin thermostat.
Liu, Jian; Li, Dezhang; Liu, Xinzijian
2016-07-14
We introduce a novel simple algorithm for thermostatting path integral molecular dynamics (PIMD) with the Langevin equation. The staging transformation of path integral beads is employed for demonstration. The optimum friction coefficients for the staging modes in the free particle limit are used for all systems. In comparison to the path integral Langevin equation thermostat, the new algorithm exploits a different order of splitting for the phase space propagator associated to the Langevin equation. While the error analysis is made for both algorithms, they are also employed in the PIMD simulations of three realistic systems (the H2O molecule, liquid para-hydrogen, and liquid water) for comparison. It is shown that the new thermostat increases the time interval of PIMD by a factor of 4-6 or more for achieving the same accuracy. In addition, the supplementary material shows the error analysis made for the algorithms when the normal-mode transformation of path integral beads is used.
A simple and accurate algorithm for path integral molecular dynamics with the Langevin thermostat
NASA Astrophysics Data System (ADS)
Liu, Jian; Li, Dezhang; Liu, Xinzijian
2016-07-01
We introduce a novel simple algorithm for thermostatting path integral molecular dynamics (PIMD) with the Langevin equation. The staging transformation of path integral beads is employed for demonstration. The optimum friction coefficients for the staging modes in the free particle limit are used for all systems. In comparison to the path integral Langevin equation thermostat, the new algorithm exploits a different order of splitting for the phase space propagator associated to the Langevin equation. While the error analysis is made for both algorithms, they are also employed in the PIMD simulations of three realistic systems (the H2O molecule, liquid para-hydrogen, and liquid water) for comparison. It is shown that the new thermostat increases the time interval of PIMD by a factor of 4-6 or more for achieving the same accuracy. In addition, the supplementary material shows the error analysis made for the algorithms when the normal-mode transformation of path integral beads is used.
Lippert, Ross A; Predescu, Cristian; Ierardi, Douglas J; Mackenzie, Kenneth M; Eastwood, Michael P; Dror, Ron O; Shaw, David E
2013-10-28
In molecular dynamics simulations, control over temperature and pressure is typically achieved by augmenting the original system with additional dynamical variables to create a thermostat and a barostat, respectively. These variables generally evolve on timescales much longer than those of particle motion, but typical integrator implementations update the additional variables along with the particle positions and momenta at each time step. We present a framework that replaces the traditional integration procedure with separate barostat, thermostat, and Newtonian particle motion updates, allowing thermostat and barostat updates to be applied infrequently. Such infrequent updates provide a particularly substantial performance advantage for simulations parallelized across many computer processors, because thermostat and barostat updates typically require communication among all processors. Infrequent updates can also improve accuracy by alleviating certain sources of error associated with limited-precision arithmetic. In addition, separating the barostat, thermostat, and particle motion update steps reduces certain truncation errors, bringing the time-average pressure closer to its target value. Finally, this framework, which we have implemented on both general-purpose and special-purpose hardware, reduces software complexity and improves software modularity.
Accurate path integral molecular dynamics simulation of ab-initio water at near-zero added cost
NASA Astrophysics Data System (ADS)
Elton, Daniel; Fritz, Michelle; Soler, José; Fernandez-Serra, Marivi
It is now established that nuclear quantum motion plays an important role in determining water's structure and dynamics. These effects are important to consider when evaluating DFT functionals and attempting to develop better ones for water. The standard way of treating nuclear quantum effects, path integral molecular dynamics (PIMD), multiplies the number of energy/force calculations by the number of beads, which is typically 32. Here we introduce a method whereby PIMD can be incorporated into a DFT molecular dynamics simulation at virtually zero cost. The method is based on the cluster (many body) expansion of the energy. We first subtract the DFT monomer energies, using a custom DFT-based monomer potential energy surface. The evolution of the PIMD beads is then performed using only the more-accurate Partridge-Schwenke monomer energy surface. The DFT calculations are done using the centroid positions. Various bead thermostats can be employed to speed up the sampling of the quantum ensemble. The method bears some resemblance to multiple timestep algorithms and other schemes used to speed up PIMD with classical force fields. We show that our method correctly captures some of key effects of nuclear quantum motion on both the structure and dynamics of water. We acknowledge support from DOE Award No. DE-FG02-09ER16052 (D.E.) and DOE Early Career Award No. DE-SC0003871 (M.V.F.S.).
NASA Astrophysics Data System (ADS)
Zhou, X. W.; Aubry, S.; Jones, R. E.; Greenstein, A.; Schelling, P. K.
2009-03-01
Significant differences exist among literature for thermal conductivity of various systems computed using molecular dynamics simulation. In some cases, unphysical results, for example, negative thermal conductivity, have been found. Using GaN as an example case and the direct nonequilibrium method, extensive molecular dynamics simulations and Monte Carlo analysis of the results have been carried out to quantify the uncertainty level of the molecular dynamics methods and to identify the conditions that can yield sufficiently accurate calculations of thermal conductivity. We found that the errors of the calculations are mainly due to the statistical thermal fluctuations. Extrapolating results to the limit of an infinite-size system tend to magnify the errors and occasionally lead to unphysical results. The error in bulk estimates can be reduced by performing longer time averages using properly selected systems over a range of sample lengths. If the errors in the conductivity estimates associated with each of the sample lengths are kept below a certain threshold, the likelihood of obtaining unphysical bulk values becomes insignificant. Using a Monte Carlo approach developed here, we have determined the probability distributions for the bulk thermal conductivities obtained using the direct method. We also have observed a nonlinear effect that can become a source of significant errors. For the extremely accurate results presented here, we predict a [0001] GaN thermal conductivity of 185W/Km at 300 K, 102W/Km at 500 K, and 74W/Km at 800 K. Using the insights obtained in the work, we have achieved a corresponding error level (standard deviation) for the bulk (infinite sample length) GaN thermal conductivity of less than 10W/Km , 5W/Km , and 15W/Km at 300 K, 500 K, and 800 K, respectively.
NASA Astrophysics Data System (ADS)
Yogurtcu, Osman N.; Johnson, Margaret E.
2015-08-01
The dynamics of association between diffusing and reacting molecular species are routinely quantified using simple rate-equation kinetics that assume both well-mixed concentrations of species and a single rate constant for parameterizing the binding rate. In two-dimensions (2D), however, even when systems are well-mixed, the assumption of a single characteristic rate constant for describing association is not generally accurate, due to the properties of diffusional searching in dimensions d ≤ 2. Establishing rigorous bounds for discriminating between 2D reactive systems that will be accurately described by rate equations with a single rate constant, and those that will not, is critical for both modeling and experimentally parameterizing binding reactions restricted to surfaces such as cellular membranes. We show here that in regimes of intrinsic reaction rate (ka) and diffusion (D) parameters ka/D > 0.05, a single rate constant cannot be fit to the dynamics of concentrations of associating species independently of the initial conditions. Instead, a more sophisticated multi-parametric description than rate-equations is necessary to robustly characterize bimolecular reactions from experiment. Our quantitative bounds derive from our new analysis of 2D rate-behavior predicted from Smoluchowski theory. Using a recently developed single particle reaction-diffusion algorithm we extend here to 2D, we are able to test and validate the predictions of Smoluchowski theory and several other theories of reversible reaction dynamics in 2D for the first time. Finally, our results also mean that simulations of reactive systems in 2D using rate equations must be undertaken with caution when reactions have ka/D > 0.05, regardless of the simulation volume. We introduce here a simple formula for an adaptive concentration dependent rate constant for these chemical kinetics simulations which improves on existing formulas to better capture non-equilibrium reaction dynamics from dilute
NASA Astrophysics Data System (ADS)
Lee, Hsing; Darden, Thomas; Pedersen, Lee
1995-09-01
Long molecular dynamics (MD) simulations for two crystal RNA dinucleotides ApU (2.0 ns) and GpC (1.5 ns) were performed, starting from the crystallographic positions of all heavy atoms in the crystals. By employing the particle-mesh-Ewald algorithm [Darden et al., J. Chem. Phys. 98 (1993) 10089] to accommodate the long-range Coulomb interactions, highly accurate MD structures were obtained for both crystals. The instantaneous root-mean-square positional deviations of the heavy atoms equilibrate at approximately 0.4 Å for both systems, while the experimental and calculated temperature factors are comparable in size. These results describe the first successful crystal MD simulation of RNA molecules.
Bai, Fang; Liao, Sha; Gu, Junfeng; Jiang, Hualiang; Wang, Xicheng; Li, Honglin
2015-04-27
Metalloproteins, particularly zinc metalloproteins, are promising therapeutic targets, and recent efforts have focused on the identification of potent and selective inhibitors of these proteins. However, the ability of current drug discovery and design technologies, such as molecular docking and molecular dynamics simulations, to probe metal-ligand interactions remains limited because of their complicated coordination geometries and rough treatment in current force fields. Herein we introduce a robust, multiobjective optimization algorithm-driven metalloprotein-specific docking program named MpSDock, which runs on a scheme similar to consensus scoring consisting of a force-field-based scoring function and a knowledge-based scoring function. For this purpose, in this study, an effective knowledge-based zinc metalloprotein-specific scoring function based on the inverse Boltzmann law was designed and optimized using a dynamic sampling and iteration optimization strategy. This optimization strategy can dynamically sample and regenerate decoy poses used in each iteration step of refining the scoring function, thus dramatically improving both the effectiveness of the exploration of the binding conformational space and the sensitivity of the ranking of the native binding poses. To validate the zinc metalloprotein-specific scoring function and its special built-in docking program, denoted MpSDockZn, an extensive comparison was performed against six universal, popular docking programs: Glide XP mode, Glide SP mode, Gold, AutoDock, AutoDock4Zn, and EADock DSS. The zinc metalloprotein-specific knowledge-based scoring function exhibited prominent performance in accurately describing the geometries and interactions of the coordination bonds between the zinc ions and chelating agents of the ligands. In addition, MpSDockZn had a competitive ability to sample and identify native binding poses with a higher success rate than the other six docking programs.
Osei-Kuffuor, Daniel; Fattebert, Jean-Luc
2014-01-01
We present the first truly scalable first-principles molecular dynamics algorithm with O(N) complexity and controllable accuracy, capable of simulating systems with finite band gaps of sizes that were previously impossible with this degree of accuracy. By avoiding global communications, we provide a practical computational scheme capable of extreme scalability. Accuracy is controlled by the mesh spacing of the finite difference discretization, the size of the localization regions in which the electronic wave functions are confined, and a cutoff beyond which the components of the overlap matrix can be omitted when computing selected elements of its inverse. We demonstrate the algorithm's excellent parallel scaling for up to 101 952 atoms on 23 328 processors, with a wall-clock time of the order of 1 min per molecular dynamics time step and numerical error on the forces of less than 7x10^{-4} Ha/Bohr.
Ladd, A.J.C.
1988-08-01
The basic methodology of equilibrium molecular dynamics is described. Examples from the literature are used to illustrate how molecular dynamics has been used to resolve theoretical controversies, provide data to test theories, and occasionally to discover new phenomena. The emphasis is on the application of molecular dynamics to an understanding of the microscopic physics underlying the transport properties of simple fluids. 98 refs., 4 figs.
NASA Astrophysics Data System (ADS)
Osei-Kuffuor, Daniel; Fattebert, Jean-Luc
2014-03-01
We present a truly scalable First-Principles Molecular Dynamics algorithm with O(N) complexity and fully controllable accuracy, capable of simulating systems of sizes that were previously impossible with this degree of accuracy. By avoiding global communication, we have extended W. Kohn's condensed matter ``nearsightedness'' principle to a practical computational scheme capable of extreme scalability. Accuracy is controlled by the mesh spacing of the finite difference discretization, the size of the localization regions in which the electronic wavefunctions are confined, and a cutoff beyond which the components of the overlap matrix can be omitted when computing selected elements of its inverse. We demonstrate the algorithm's excellent parallel scaling for up to 100,000 atoms on 100,000 processors, with a wall-clock time of the order of one minute per molecular dynamics time step. This work was performed under the auspices of the U.S. Department of Energy by Lawrence Livermore National Laboratory under Contract DE-AC52-07NA27344.
Riahi, Saleh; Rowley, Christopher N
2014-10-30
The quantum mechanical (QM)/molecular mechanical (MM) interface between Chemistry at HARvard Molecular Mechanics (CHARMM) and TURBOMOLE is described. CHARMM provides an extensive set of simulation algorithms, like molecular dynamics (MD) and free energy perturbation, and support for mature nonpolarizable and Drude polarizable force fields. TURBOMOLE provides fast QM calculations using density functional theory or wave function methods and excited state properties. CHARMM-TURBOMOLE is well-suited for extended QM/MM MD simulations using first principles methods with large (triple-ζ) basis sets. We demonstrate these capabilities with a QM/MM simulation of Mg(2+) (aq), where the MM outer sphere water molecules are represented using the SWM4-NDP Drude polarizable force field and the ion and inner coordination sphere are represented using QM PBE, PBE0, and MP2 methods. The relative solvation free energies of Mg(2+) and Zn(2+) were calculated using thermodynamic integration. We also demonstrate the features for excited state properties. We calculate the time-averaged solution absorption spectrum of indole, the emission spectrum of the indole 1La excited state, and the electronic circular dichroism spectrum of an oxacepham.
Beuc, R.; Movre, M.; Horvatic, V.; Vadla, C.; Dulieu, O.; Aymar, M.
2007-03-15
Experimental studies of the absorption spectrum of the Rb{sub 2} dimer are performed in the 600-1100 nm wavelength range for temperatures between 615 and 745 K. The reduced absorption coefficient is measured by spatially resolved white light absorption in overheated rubidium vapor with a radial temperature gradient, which enables simultaneous measurements at different temperatures. Semiclassical and quantum spectral simulations are obtained by taking into account all possible transitions involving the potential curves stemming from the 5 {sup 2}S+5 {sup 2}S and 5 {sup 2}S+5 {sup 2}P asymptotes. The most accurate experimental potential curves are used where available, and newly calculated potential curves and transition dipole moments otherwise. The overall consistency of the theoretical model with the experimental interpretation is obtained only if the radial dependence of both the calculated transition dipole moments and the spin-orbit coupling is taken into account. This highlights the low-resolution absorption spectroscopy as a valuable tool for checking the accuracy of molecular electronic structure calculations.
NASA Astrophysics Data System (ADS)
Genova, Alessandro; Ceresoli, Davide; Pavanello, Michele
2016-06-01
In this work we achieve three milestones: (1) we present a subsystem DFT method capable of running ab-initio molecular dynamics simulations accurately and efficiently. (2) In order to rid the simulations of inter-molecular self-interaction error, we exploit the ability of semilocal frozen density embedding formulation of subsystem DFT to represent the total electron density as a sum of localized subsystem electron densities that are constrained to integrate to a preset, constant number of electrons; the success of the method relies on the fact that employed semilocal nonadditive kinetic energy functionals effectively cancel out errors in semilocal exchange-correlation potentials that are linked to static correlation effects and self-interaction. (3) We demonstrate this concept by simulating liquid water and solvated OH• radical. While the bulk of our simulations have been performed on a periodic box containing 64 independent water molecules for 52 ps, we also simulated a box containing 256 water molecules for 22 ps. The results show that, provided one employs an accurate nonadditive kinetic energy functional, the dynamics of liquid water and OH• radical are in semiquantitative agreement with experimental results or higher-level electronic structure calculations. Our assessments are based upon comparisons of radial and angular distribution functions as well as the diffusion coefficient of the liquid.
Meng, Qingyong; Chen, Jun; Zhang, Dong H
2015-09-14
The ring polymer molecular dynamics (RPMD) calculations are performed to calculate rate constants for the title reaction on the recently constructed potential energy surface based on permutation invariant polynomial (PIP) neural-network (NN) fitting [J. Li et al., J. Chem. Phys. 142, 204302 (2015)]. By inspecting convergence, 16 beads are used in computing free-energy barriers at 300 K ≤ T ≤ 1000 K, while different numbers of beads are used for transmission coefficients. The present RPMD rates are in excellent agreement with quantum rates computed on the same potential energy surface, as well as with the experimental measurements, demonstrating further that the RPMD is capable of producing accurate rates for polyatomic chemical reactions even at rather low temperatures.
NASA Astrophysics Data System (ADS)
Meng, Qingyong; Chen, Jun; Zhang, Dong H.
2015-09-01
The ring polymer molecular dynamics (RPMD) calculations are performed to calculate rate constants for the title reaction on the recently constructed potential energy surface based on permutation invariant polynomial (PIP) neural-network (NN) fitting [J. Li et al., J. Chem. Phys. 142, 204302 (2015)]. By inspecting convergence, 16 beads are used in computing free-energy barriers at 300 K ≤ T ≤ 1000 K, while different numbers of beads are used for transmission coefficients. The present RPMD rates are in excellent agreement with quantum rates computed on the same potential energy surface, as well as with the experimental measurements, demonstrating further that the RPMD is capable of producing accurate rates for polyatomic chemical reactions even at rather low temperatures.
Willow, Soohaeng Yoo; Salim, Michael A.; Kim, Kwang S.; Hirata, So
2015-01-01
A direct, simultaneous calculation of properties of a liquid using an ab initio electron-correlated theory has long been unthinkable. Here we present structural, dynamical, and response properties of liquid water calculated by ab initio molecular dynamics using the embedded-fragment spin-component-scaled second-order many-body perturbation method with the aug-cc-pVDZ basis set. This level of theory is chosen as it accurately and inexpensively reproduces the water dimer potential energy surface from the coupled-cluster singles, doubles, and noniterative triples with the aug-cc-pVQZ basis set, which is nearly exact. The calculated radial distribution function, self-diffusion coefficient, coordinate number, and dipole moment, as well as the infrared and Raman spectra are in excellent agreement with experimental results. The shapes and widths of the OH stretching bands in the infrared and Raman spectra and their isotropic-anisotropic Raman noncoincidence, which reflect the diverse local hydrogen-bond environment, are also reproduced computationally. The simulation also reveals intriguing dynamic features of the environment, which are difficult to probe experimentally, such as a surprisingly large fluctuation in the coordination number and the detailed mechanism by which the hydrogen donating water molecules move across the first and second shells, thereby causing this fluctuation. PMID:26400690
Willow, Soohaeng Yoo; Salim, Michael A; Kim, Kwang S; Hirata, So
2015-01-01
A direct, simultaneous calculation of properties of a liquid using an ab initio electron-correlated theory has long been unthinkable. Here we present structural, dynamical, and response properties of liquid water calculated by ab initio molecular dynamics using the embedded-fragment spin-component-scaled second-order many-body perturbation method with the aug-cc-pVDZ basis set. This level of theory is chosen as it accurately and inexpensively reproduces the water dimer potential energy surface from the coupled-cluster singles, doubles, and noniterative triples with the aug-cc-pVQZ basis set, which is nearly exact. The calculated radial distribution function, self-diffusion coefficient, coordinate number, and dipole moment, as well as the infrared and Raman spectra are in excellent agreement with experimental results. The shapes and widths of the OH stretching bands in the infrared and Raman spectra and their isotropic-anisotropic Raman noncoincidence, which reflect the diverse local hydrogen-bond environment, are also reproduced computationally. The simulation also reveals intriguing dynamic features of the environment, which are difficult to probe experimentally, such as a surprisingly large fluctuation in the coordination number and the detailed mechanism by which the hydrogen donating water molecules move across the first and second shells, thereby causing this fluctuation.
Fang, Changming; Li, Wun-Fan; Koster, Rik S; Klimeš, Jiří; van Blaaderen, Alfons; van Huis, Marijn A
2015-01-01
Knowledge about the intrinsic electronic properties of water is imperative for understanding the behaviour of aqueous solutions that are used throughout biology, chemistry, physics, and industry. The calculation of the electronic band gap of liquids is challenging, because the most accurate ab initio approaches can be applied only to small numbers of atoms, while large numbers of atoms are required for having configurations that are representative of a liquid. Here we show that a high-accuracy value for the electronic band gap of water can be obtained by combining beyond-DFT methods and statistical time-averaging. Liquid water is simulated at 300 K using a plane-wave density functional theory molecular dynamics (PW-DFT-MD) simulation and a van der Waals density functional (optB88-vdW). After applying a self-consistent GW correction the band gap of liquid water at 300 K is calculated as 7.3 eV, in good agreement with recent experimental observations in the literature (6.9 eV). For simulations of phase transformations and chemical reactions in water or aqueous solutions whereby an accurate description of the electronic structure is required, we suggest to use these advanced GW corrections in combination with the statistical analysis of quantum mechanical MD simulations.
Accurate Molecular Polarizabilities Based on Continuum Electrostatics
Truchon, Jean-François; Nicholls, Anthony; Iftimie, Radu I.; Roux, Benoît; Bayly, Christopher I.
2013-01-01
A novel approach for representing the intramolecular polarizability as a continuum dielectric is introduced to account for molecular electronic polarization. It is shown, using a finite-difference solution to the Poisson equation, that the Electronic Polarization from Internal Continuum (EPIC) model yields accurate gas-phase molecular polarizability tensors for a test set of 98 challenging molecules composed of heteroaromatics, alkanes and diatomics. The electronic polarization originates from a high intramolecular dielectric that produces polarizabilities consistent with B3LYP/aug-cc-pVTZ and experimental values when surrounded by vacuum dielectric. In contrast to other approaches to model electronic polarization, this simple model avoids the polarizability catastrophe and accurately calculates molecular anisotropy with the use of very few fitted parameters and without resorting to auxiliary sites or anisotropic atomic centers. On average, the unsigned error in the average polarizability and anisotropy compared to B3LYP are 2% and 5%, respectively. The correlation between the polarizability components from B3LYP and this approach lead to a R2 of 0.990 and a slope of 0.999. Even the F2 anisotropy, shown to be a difficult case for existing polarizability models, can be reproduced within 2% error. In addition to providing new parameters for a rapid method directly applicable to the calculation of polarizabilities, this work extends the widely used Poisson equation to areas where accurate molecular polarizabilities matter. PMID:23646034
NASA Astrophysics Data System (ADS)
Meng, Qingyong; Chen, Jun; Zhang, Dong H.
2016-04-01
To fast and accurately compute rate coefficients of the H/D + CH4 → H2/HD + CH3 reactions, we propose a segmented strategy for fitting suitable potential energy surface (PES), on which ring-polymer molecular dynamics (RPMD) simulations are performed. On the basis of recently developed permutation invariant polynomial neural-network approach [J. Li et al., J. Chem. Phys. 142, 204302 (2015)], PESs in local configuration spaces are constructed. In this strategy, global PES is divided into three parts, including asymptotic, intermediate, and interaction parts, along the reaction coordinate. Since less fitting parameters are involved in the local PESs, the computational efficiency for operating the PES routine is largely enhanced by a factor of ˜20, comparing with that for global PES. On interaction part, the RPMD computational time for the transmission coefficient can be further efficiently reduced by cutting off the redundant part of the child trajectories. For H + CH4, good agreements among the present RPMD rates and those from previous simulations as well as experimental results are found. For D + CH4, on the other hand, qualitative agreement between present RPMD and experimental results is predicted.
Cheng, Xiaolin; Ivanov, Ivaylo
2012-01-01
Molecular dynamics (MD) simulation holds the promise of revealing the mechanisms of biological processes in their ultimate detail. It is carried out by computing the interaction forces acting on each atom and then propagating the velocities and positions of the atoms by numerical integration of Newton's equations of motion. In this review, we present an overview of how the MD simulation can be conducted to address computational toxicity problems. The study cases will cover a standard MD simulation performed to investigate the overall flexibility of a cytochrome P450 (CYP) enzyme and a set of more advanced MD simulations to examine the barrier to ion conduction in a human α7 nicotinic acetylcholine receptor (nAChR).
Jiménez-Osés, Gonzalo; García, José I; Corzana, Francisco; Elguero, José
2011-05-20
A new protocol combining classical MD simulations and DFT calculations is presented to accurately estimate the (1)H NMR chemical shifts of highly mobile guest-host systems and their thermal dependence. This strategy has been successfully applied for the hydrogen molecule trapped into C(60) fullerene, an unresolved and challenging prototypical case for which experimental values have never been reproduced. The dependence of the final values on the theoretical method and their implications to avoid over interpretation of the obtained results are carefully described.
Multiscale reactive molecular dynamics
Knight, Chris; Lindberg, Gerrick E.; Voth, Gregory A.
2012-01-01
Many processes important to chemistry, materials science, and biology cannot be described without considering electronic and nuclear-level dynamics and their coupling to slower, cooperative motions of the system. These inherently multiscale problems require computationally efficient and accurate methods to converge statistical properties. In this paper, a method is presented that uses data directly from condensed phase ab initio simulations to develop reactive molecular dynamics models that do not require predefined empirical functions. Instead, the interactions used in the reactive model are expressed as linear combinations of interpolating functions that are optimized by using a linear least-squares algorithm. One notable benefit of the procedure outlined here is the capability to minimize the number of parameters requiring nonlinear optimization. The method presented can be generally applied to multiscale problems and is demonstrated by generating reactive models for the hydrated excess proton and hydroxide ion based directly on condensed phase ab initio molecular dynamics simulations. The resulting models faithfully reproduce the water-ion structural properties and diffusion constants from the ab initio simulations. Additionally, the free energy profiles for proton transfer, which is sensitive to the structural diffusion of both ions in water, are reproduced. The high fidelity of these models to ab initio simulations will permit accurate modeling of general chemical reactions in condensed phase systems with computational efficiency orders of magnitudes greater than currently possible with ab initio simulation methods, thus facilitating a proper statistical sampling of the coupling to slow, large-scale motions of the system. PMID:23249062
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.
Le, Hung M; Dinh, Thach S; Le, Hieu V
2011-10-13
The singlet-triplet transformation and molecular dissociation of ozone (O(3)) gas is investigated by performing quasi-classical molecular dynamics (MD) simulations on an ab initio potential energy surface (PES) with visible and near-infrared excitations. MP4(SDQ) level of theory with the 6-311g(2d,2p) basis set is executed for three different electronic spin states (singlet, triplet, and quintet). In order to simplify the potential energy function, an approximation is adopted by ignoring the spin-orbit coupling and allowing the molecule to switch favorably and instantaneously to the spin state that is more energetically stable (lowest in energy among the three spin states). This assumption has previously been utilized to study the SiO(2) system as reported by Agrawal et al. (J. Chem. Phys. 2006, 124 (13), 134306). The use of such assumption in this study probably makes the upper limits of computed rate coefficients the true rate coefficients. The global PES for ozone is constructed by fitting 5906 ab initio data points using a 60-neuron two-layer feed-forward neural network. The mean-absolute error and root-mean-squared error of this fit are 0.0446 eV (1.03 kcal/mol) and 0.0756 eV (1.74 kcal/mol), respectively, which reveal very good fitting accuracy. The parameter coefficients of the global PES are reported in this paper. In order to identify the spin state with high confidence, we propose the use of a pattern-recognition neural network, which is trained to predict the spin state of a given configuration (with a prediction accuracy being 95.6% on a set of testing data points). To enhance the prediction effectiveness, a buffer series of five points are validated to confirm the spin state during the MD process to gain better confidence. Quasi-classical MD simulations from 1.2 to 2.4 eV of total internal energy (including zero-point energy) result in rate coefficients of singlet-triplet transformation in the range of 0.027 ps(-1) to 1.21 ps(-1). Also, we find very
Accelerated molecular dynamics methods
Perez, Danny
2011-01-04
The molecular dynamics method, although extremely powerful for materials simulations, is limited to times scales of roughly one microsecond or less. On longer time scales, dynamical evolution typically consists of infrequent events, which are usually activated processes. This course is focused on understanding infrequent-event dynamics, on methods for characterizing infrequent-event mechanisms and rate constants, and on methods for simulating long time scales in infrequent-event systems, emphasizing the recently developed accelerated molecular dynamics methods (hyperdynamics, parallel replica dynamics, and temperature accelerated dynamics). Some familiarity with basic statistical mechanics and molecular dynamics methods will be assumed.
Towards Accurate Molecular Modeling of Plastic Bonded Explosives
NASA Astrophysics Data System (ADS)
Chantawansri, T. L.; Andzelm, J.; Taylor, D.; Byrd, E.; Rice, B.
2010-03-01
There is substantial interest in identifying the controlling factors that influence the susceptibility of polymer bonded explosives (PBXs) to accidental initiation. Numerous Molecular Dynamics (MD) simulations of PBXs using the COMPASS force field have been reported in recent years, where the validity of the force field in modeling the solid EM fill has been judged solely on its ability to reproduce lattice parameters, which is an insufficient metric. Performance of the COMPASS force field in modeling EMs and the polymeric binder has been assessed by calculating structural, thermal, and mechanical properties, where only fair agreement with experimental data is obtained. We performed MD simulations using the COMPASS force field for the polymer binder hydroxyl-terminated polybutadiene and five EMs: cyclotrimethylenetrinitramine, 1,3,5,7-tetranitro-1,3,5,7-tetra-azacyclo-octane, 2,4,6,8,10,12-hexantirohexaazazisowurzitane, 2,4,6-trinitro-1,3,5-benzenetriamine, and pentaerythritol tetranitate. Predicted EM crystallographic and molecular structural parameters, as well as calculated properties for the binder will be compared with experimental results for different simulation conditions. We also present novel simulation protocols, which improve agreement between experimental and computation results thus leading to the accurate modeling of PBXs.
Kapil, V; VandeVondele, J; Ceriotti, M
2016-02-01
The development and implementation of increasingly accurate methods for electronic structure calculations mean that, for many atomistic simulation problems, treating light nuclei as classical particles is now one of the most serious approximations. Even though recent developments have significantly reduced the overhead for modeling the quantum nature of the nuclei, the cost is still prohibitive when combined with advanced electronic structure methods. Here we present how multiple time step integrators can be combined with ring-polymer contraction techniques (effectively, multiple time stepping in imaginary time) to reduce virtually to zero the overhead of modelling nuclear quantum effects, while describing inter-atomic forces at high levels of electronic structure theory. This is demonstrated for a combination of MP2 and semi-local DFT applied to the Zundel cation. The approach can be seamlessly combined with other methods to reduce the computational cost of path integral calculations, such as high-order factorizations of the Boltzmann operator or generalized Langevin equation thermostats.
NASA Astrophysics Data System (ADS)
Kapil, V.; VandeVondele, J.; Ceriotti, M.
2016-02-01
The development and implementation of increasingly accurate methods for electronic structure calculations mean that, for many atomistic simulation problems, treating light nuclei as classical particles is now one of the most serious approximations. Even though recent developments have significantly reduced the overhead for modeling the quantum nature of the nuclei, the cost is still prohibitive when combined with advanced electronic structure methods. Here we present how multiple time step integrators can be combined with ring-polymer contraction techniques (effectively, multiple time stepping in imaginary time) to reduce virtually to zero the overhead of modelling nuclear quantum effects, while describing inter-atomic forces at high levels of electronic structure theory. This is demonstrated for a combination of MP2 and semi-local DFT applied to the Zundel cation. The approach can be seamlessly combined with other methods to reduce the computational cost of path integral calculations, such as high-order factorizations of the Boltzmann operator or generalized Langevin equation thermostats.
Meng, Qingyong Chen, Jun Zhang, Dong H.
2015-09-14
The ring polymer molecular dynamics (RPMD) calculations are performed to calculate rate constants for the title reaction on the recently constructed potential energy surface based on permutation invariant polynomial (PIP) neural-network (NN) fitting [J. Li et al., J. Chem. Phys. 142, 204302 (2015)]. By inspecting convergence, 16 beads are used in computing free-energy barriers at 300 K ≤ T ≤ 1000 K, while different numbers of beads are used for transmission coefficients. The present RPMD rates are in excellent agreement with quantum rates computed on the same potential energy surface, as well as with the experimental measurements, demonstrating further that the RPMD is capable of producing accurate rates for polyatomic chemical reactions even at rather low temperatures.
Laasonen, Kari
2013-01-01
In this chapter, an introduction to ab initio molecular dynamics (AIMD) has been given. Many of the basic concepts, like the Hellman-Feynman forces, the difference between the Car-Parrinello molecular dynamics and AIMD, have been explained. Also a very versatile AIMD code, the CP2K, has been introduced. On the application, the emphasis was on the aqueous systems and chemical reactions. The biochemical applications have not been discussed in depth.
A sampling of molecular dynamics
NASA Astrophysics Data System (ADS)
Sindhikara, Daniel Jon
The sheer vastness of the number of computations required to simulate a biological molecule puts incredible pressure on algorithms to be efficient while maintaining sufficient accuracy. This dissertation summarizes various projects whose purposes address the large span of types of problems in molecular dynamics simulations of biological systems including: increasing efficiency, measuring convergence, avoiding pitfalls, and an application and analysis of a biological system. Chapters 3 and 4 deal with an enhanced sampling algorithm called "replica exchange molecular dynamics" which is designed to speed-up molecular dynamics simulations. The optimization of a key parameter of these simulations is analyzed. In these successive projects, it was found conclusively that maximizing "exchange attempt frequency" is the most efficient way to run a replica exchange molecular dynamics simulation. Chapter 5 describes an enhanced metric for convergence in parallel simulations called the normalized ergodic measure. The metric is applied to several properties for several replica exchange simulations. Advantages of this metric over other methods are described. Chapter 6 describes the implementation and optimization of an enhanced sampling algorithm similar to replica exchange molecular dynamics called multicanonical algorithm replica exchange molecular dynamics. The algorithm was implemented into a biomolecular simulation suite called AMBER. Additionally several parameters were analyzed and optimized. In Chapter 7, a pitfall in molecular dynamics is observed in biological systems that is caused by negligent use of a simulation's "thermostat". It was found that if the same pseudorandom number seed were used for multiple systems, they eventually synchronize. In this project, synchronization was observed in biological molecules. Various negative effects including corruption of data are pointed out. Chapter 8 describes molecular dynamics simulation of NikR, a homotetrameric nickel
Substructured multibody molecular dynamics.
Grest, Gary Stephen; Stevens, Mark Jackson; Plimpton, Steven James; Woolf, Thomas B. (Johns Hopkins University, Baltimore, MD); Lehoucq, Richard B.; Crozier, Paul Stewart; Ismail, Ahmed E.; Mukherjee, Rudranarayan M. (Rensselaer Polytechnic Institute, Troy, NY); Draganescu, Andrei I.
2006-11-01
We have enhanced our parallel molecular dynamics (MD) simulation software LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator, lammps.sandia.gov) to include many new features for accelerated simulation including articulated rigid body dynamics via coupling to the Rensselaer Polytechnic Institute code POEMS (Parallelizable Open-source Efficient Multibody Software). We use new features of the LAMMPS software package to investigate rhodopsin photoisomerization, and water model surface tension and capillary waves at the vapor-liquid interface. Finally, we motivate the recipes of MD for practitioners and researchers in numerical analysis and computational mechanics.
From molecular dynamics to Brownian dynamics
Erban, Radek
2014-01-01
Three coarse-grained molecular dynamics (MD) models are investigated with the aim of developing and analysing multi-scale methods which use MD simulations in parts of the computational domain and (less detailed) Brownian dynamics (BD) simulations in the remainder of the domain. The first MD model is formulated in one spatial dimension. It is based on elastic collisions of heavy molecules (e.g. proteins) with light point particles (e.g. water molecules). Two three-dimensional MD models are then investigated. The obtained results are applied to a simplified model of protein binding to receptors on the cellular membrane. It is shown that modern BD simulators of intracellular processes can be used in the bulk and accurately coupled with a (more detailed) MD model of protein binding which is used close to the membrane. PMID:25002825
A robust and accurate formulation of molecular and colloidal electrostatics
NASA Astrophysics Data System (ADS)
Sun, Qiang; Klaseboer, Evert; Chan, Derek Y. C.
2016-08-01
This paper presents a re-formulation of the boundary integral method for the Debye-Hückel model of molecular and colloidal electrostatics that removes the mathematical singularities that have to date been accepted as an intrinsic part of the conventional boundary integral equation method. The essence of the present boundary regularized integral equation formulation consists of subtracting a known solution from the conventional boundary integral method in such a way as to cancel out the singularities associated with the Green's function. This approach better reflects the non-singular physical behavior of the systems on boundaries with the benefits of the following: (i) the surface integrals can be evaluated accurately using quadrature without any need to devise special numerical integration procedures, (ii) being able to use quadratic or spline function surface elements to represent the surface more accurately and the variation of the functions within each element is represented to a consistent level of precision by appropriate interpolation functions, (iii) being able to calculate electric fields, even at boundaries, accurately and directly from the potential without having to solve hypersingular integral equations and this imparts high precision in calculating the Maxwell stress tensor and consequently, intermolecular or colloidal forces, (iv) a reliable way to handle geometric configurations in which different parts of the boundary can be very close together without being affected by numerical instabilities, therefore potentials, fields, and forces between surfaces can be found accurately at surface separations down to near contact, and (v) having the simplicity of a formulation that does not require complex algorithms to handle singularities will result in significant savings in coding effort and in the reduction of opportunities for coding errors. These advantages are illustrated using examples drawn from molecular and colloidal electrostatics.
A robust and accurate formulation of molecular and colloidal electrostatics.
Sun, Qiang; Klaseboer, Evert; Chan, Derek Y C
2016-08-01
This paper presents a re-formulation of the boundary integral method for the Debye-Hückel model of molecular and colloidal electrostatics that removes the mathematical singularities that have to date been accepted as an intrinsic part of the conventional boundary integral equation method. The essence of the present boundary regularized integral equation formulation consists of subtracting a known solution from the conventional boundary integral method in such a way as to cancel out the singularities associated with the Green's function. This approach better reflects the non-singular physical behavior of the systems on boundaries with the benefits of the following: (i) the surface integrals can be evaluated accurately using quadrature without any need to devise special numerical integration procedures, (ii) being able to use quadratic or spline function surface elements to represent the surface more accurately and the variation of the functions within each element is represented to a consistent level of precision by appropriate interpolation functions, (iii) being able to calculate electric fields, even at boundaries, accurately and directly from the potential without having to solve hypersingular integral equations and this imparts high precision in calculating the Maxwell stress tensor and consequently, intermolecular or colloidal forces, (iv) a reliable way to handle geometric configurations in which different parts of the boundary can be very close together without being affected by numerical instabilities, therefore potentials, fields, and forces between surfaces can be found accurately at surface separations down to near contact, and (v) having the simplicity of a formulation that does not require complex algorithms to handle singularities will result in significant savings in coding effort and in the reduction of opportunities for coding errors. These advantages are illustrated using examples drawn from molecular and colloidal electrostatics. PMID:27497538
Open boundary molecular dynamics
NASA Astrophysics Data System (ADS)
Delgado-Buscalioni, R.; Sablić, J.; Praprotnik, M.
2015-09-01
This contribution analyzes several strategies and combination of methodologies to perform molecular dynamic simulations in open systems. Here, the term open indicates that the total system has boundaries where transfer of mass, momentum and energy can take place. This formalism, which we call Open Boundary Molecular Dynamics (OBMD), can act as interface of different schemes, such as Adaptive Resolution Scheme (AdResS) and Hybrid continuum-particle dynamics to link atomistic, coarse-grained (CG) and continuum (Eulerian) fluid dynamics in the general framework of fluctuating Navier-Stokes equations. The core domain of the simulation box is solved using all-atom descriptions. The CG layer introduced using AdResS is located at the outer part of the open box to make feasible the insertion of large molecules into the system. Communications between the molecular system and the outer world are carried out in the outer layers, called buffers. These coupling preserve momentum and mass conservation laws and can thus be linked with Eulerian hydro- dynamic solvers. In its simpler form, OBMD allows, however, to impose a local pressure tensor and a heat flux across the system's boundaries. For a one component molecular system, the external normal pressure and temperature determine the external chemical potential and thus the independent parameters of a grand-canonical ensemble simulation. Extended ensembles under non-equilibrium stationary states can also be simulated as well as time dependent forcings (e.g. oscillatory rheology). To illustrate the robustness of the combined OBMD-AdResS method, we present simulations of star-polymer melts at equilibrium and in sheared flow.
Accurate Evaluation Method of Molecular Binding Affinity from Fluctuation Frequency
NASA Astrophysics Data System (ADS)
Hoshino, Tyuji; Iwamoto, Koji; Ode, Hirotaka; Ohdomari, Iwao
2008-05-01
Exact estimation of the molecular binding affinity is significantly important for drug discovery. The energy calculation is a direct method to compute the strength of the interaction between two molecules. This energetic approach is, however, not accurate enough to evaluate a slight difference in binding affinity when distinguishing a prospective substance from dozens of candidates for medicine. Hence more accurate estimation of drug efficacy in a computer is currently demanded. Previously we proposed a concept of estimating molecular binding affinity, focusing on the fluctuation at an interface between two molecules. The aim of this paper is to demonstrate the compatibility between the proposed computational technique and experimental measurements, through several examples for computer simulations of an association of human immunodeficiency virus type-1 (HIV-1) protease and its inhibitor (an example for a drug-enzyme binding), a complexation of an antigen and its antibody (an example for a protein-protein binding), and a combination of estrogen receptor and its ligand chemicals (an example for a ligand-receptor binding). The proposed affinity estimation has proven to be a promising technique in the advanced stage of the discovery and the design of drugs.
Molecular dynamics simulations.
Lindahl, Erik
2015-01-01
Molecular dynamics has evolved from a niche method mainly applicable to model systems into a cornerstone in molecular biology. It provides us with a powerful toolbox that enables us to follow and understand structure and dynamics with extreme detail-literally on scales where individual atoms can be tracked. However, with great power comes great responsibility: Simulations will not magically provide valid results, but it requires a skilled researcher. This chapter introduces you to this, and makes you aware of some potential pitfalls. We focus on the two basic and most used methods; optimizing a structure with energy minimization and simulating motion with molecular dynamics. The statistical mechanics theory is covered briefly as well as limitations, for instance the lack of quantum effects and short timescales. As a practical example, we show each step of a simulation of a small protein, including examples of hardware and software, how to obtain a starting structure, immersing it in water, and choosing good simulation parameters. You will learn how to analyze simulations in terms of structure, fluctuations, geometrical features, and how to create ray-traced movies for presentations. With modern GPU acceleration, a desktop can perform μs-scale simulations of small proteins in a day-only 15 years ago this took months on the largest supercomputer in the world. As a final exercise, we show you how to set up, perform, and interpret such a folding simulation.
Molecular dynamics simulations.
Lindahl, Erik R
2008-01-01
Molecular simulation is a very powerful toolbox in modern molecular modeling, and enables us to follow and understand structure and dynamics with extreme detail--literally on scales where motion of individual atoms can be tracked. This chapter focuses on the two most commonly used methods, namely, energy minimization and molecular dynamics, that, respectively, optimize structure and simulate the natural motion of biological macromolecules. The common theoretical framework based on statistical mechanics is covered briefly as well as limitations of the computational approach, for instance, the lack of quantum effects and limited timescales accessible. As a practical example, a full simulation of the protein lysozyme in water is described step by step, including examples of necessary hardware and software, how to obtain suitable starting molecular structures, immersing it in a solvent, choosing good simulation parameters, and energy minimization. The chapter also describes how to analyze the simulation in terms of potential energies, structural fluctuations, coordinate stability, geometrical features, and, finally, how to create beautiful ray-traced movies that can be used in presentations.
Interactive molecular dynamics
NASA Astrophysics Data System (ADS)
Schroeder, Daniel V.
2015-03-01
Physics students now have access to interactive molecular dynamics simulations that can model and animate the motions of hundreds of particles, such as noble gas atoms, that attract each other weakly at short distances but repel strongly when pressed together. Using these simulations, students can develop an understanding of forces and motions at the molecular scale, nonideal fluids, phases of matter, thermal equilibrium, nonequilibrium states, the Boltzmann distribution, the arrow of time, and much more. This article summarizes the basic features and capabilities of such a simulation, presents a variety of student exercises using it at the introductory and intermediate levels, and describes some enhancements that can further extend its uses. A working simulation code, in html5 and javascript for running within any modern Web browser, is provided as an online supplement.
Introduction to Accelerated Molecular Dynamics
Perez, Danny
2012-07-10
Molecular Dynamics is the numerical solution of the equations of motion of a set of atoms, given an interatomic potential V and some boundary and initial conditions. Molecular Dynamics is the largest scale model that gives unbiased dynamics [x(t),p(t)] in full atomistic detail. Molecular Dynamics: is simple; is 'exact' for classical dynamics (with respect to a given V); can be used to compute any (atomistic) thermodynamical or dynamical properties; naturally handles complexity -- the system does the right thing at the right time. The physics derives only from the interatomic potential.
Accurately measuring dynamic coefficient of friction in ultraform finishing
NASA Astrophysics Data System (ADS)
Briggs, Dennis; Echaves, Samantha; Pidgeon, Brendan; Travis, Nathan; Ellis, Jonathan D.
2013-09-01
UltraForm Finishing (UFF) is a deterministic sub-aperture computer numerically controlled grinding and polishing platform designed by OptiPro Systems. UFF is used to grind and polish a variety of optics from simple spherical to fully freeform, and numerous materials from glasses to optical ceramics. The UFF system consists of an abrasive belt around a compliant wheel that rotates and contacts the part to remove material. This work aims to accurately measure the dynamic coefficient of friction (μ), how it changes as a function of belt wear, and how this ultimately affects material removal rates. The coefficient of friction has been examined in terms of contact mechanics and Preston's equation to determine accurate material removal rates. By accurately predicting changes in μ, polishing iterations can be more accurately predicted, reducing the total number of iterations required to meet specifications. We have established an experimental apparatus that can accurately measure μ by measuring triaxial forces during translating loading conditions or while manufacturing the removal spots used to calculate material removal rates. Using this system, we will demonstrate μ measurements for UFF belts during different states of their lifecycle and assess the material removal function from spot diagrams as a function of wear. Ultimately, we will use this system for qualifying belt-wheel-material combinations to develop a spot-morphing model to better predict instantaneous material removal functions.
NASA Astrophysics Data System (ADS)
Heaps, Charles W.; Mazziotti, David A.
2016-08-01
Quantum molecular dynamics requires an accurate representation of the molecular potential energy surface from a minimal number of electronic structure calculations, particularly for nonadiabatic dynamics where excited states are required. In this paper, we employ pseudospectral sampling of time-dependent Gaussian basis functions for the simulation of non-adiabatic dynamics. Unlike other methods, the pseudospectral Gaussian molecular dynamics tests the Schrödinger equation with N Dirac delta functions located at the centers of the Gaussian functions reducing the scaling of potential energy evaluations from O ( N 2 ) to O ( N ) . By projecting the Gaussian basis onto discrete points in space, the method is capable of efficiently and quantitatively describing the nonadiabatic population transfer and intra-surface quantum coherence. We investigate three model systems: the photodissociation of three coupled Morse oscillators, the bound state dynamics of two coupled Morse oscillators, and a two-dimensional model for collinear triatomic vibrational dynamics. In all cases, the pseudospectral Gaussian method is in quantitative agreement with numerically exact calculations. The results are promising for nonadiabatic molecular dynamics in molecular systems where strongly correlated ground or excited states require expensive electronic structure calculations.
Accurate measurements of dynamics and reproducibility in small genetic networks
Dubuis, Julien O; Samanta, Reba; Gregor, Thomas
2013-01-01
Quantification of gene expression has become a central tool for understanding genetic networks. In many systems, the only viable way to measure protein levels is by immunofluorescence, which is notorious for its limited accuracy. Using the early Drosophila embryo as an example, we show that careful identification and control of experimental error allows for highly accurate gene expression measurements. We generated antibodies in different host species, allowing for simultaneous staining of four Drosophila gap genes in individual embryos. Careful error analysis of hundreds of expression profiles reveals that less than ∼20% of the observed embryo-to-embryo fluctuations stem from experimental error. These measurements make it possible to extract not only very accurate mean gene expression profiles but also their naturally occurring fluctuations of biological origin and corresponding cross-correlations. We use this analysis to extract gap gene profile dynamics with ∼1 min accuracy. The combination of these new measurements and analysis techniques reveals a twofold increase in profile reproducibility owing to a collective network dynamics that relays positional accuracy from the maternal gradients to the pair-rule genes. PMID:23340845
Molecular photoionization dynamics
Dehmer, Joseph L.
1982-05-01
This program seeks to develop both physical insight and quantitative characterization of molecular photoionization processes. Progress is briefly described, and some publications resulting from the research are listed. (WHK)
Romanov, V N; Cygan, R T; Myshakin, E M
2012-06-21
Naturally occurring clay minerals provide a distinctive material for carbon capture and carbon dioxide sequestration. Swelling clay minerals, such as the smectite variety, possess an aluminosilicate structure that is controlled by low-charge layers that readily expand to accommodate water molecules and, potentially, CO2. Recent experimental studies have demonstrated the efficacy of intercalating CO2 in the interlayer of layered clays, but little is known about the molecular mechanisms of the process and the extent of carbon capture as a function of clay charge and structure. A series of molecular dynamics simulations and vibrational analyses have been completed to assess the molecular interactions associated with incorporation of CO2 and H2O in the interlayer of montmorillonite clay and to help validate the models with experimental observation. An accurate and fully flexible set of interatomic potentials for CO2 is developed and combined with Clayff potentials to help evaluate the intercalation mechanism and examine the effect of molecular flexibility onthe diffusion rate of CO2 in water.
Building dynamic population graph for accurate correspondence detection.
Du, Shaoyi; Guo, Yanrong; Sanroma, Gerard; Ni, Dong; Wu, Guorong; Shen, Dinggang
2015-12-01
In medical imaging studies, there is an increasing trend for discovering the intrinsic anatomical difference across individual subjects in a dataset, such as hand images for skeletal bone age estimation. Pair-wise matching is often used to detect correspondences between each individual subject and a pre-selected model image with manually-placed landmarks. However, the large anatomical variability across individual subjects can easily compromise such pair-wise matching step. In this paper, we present a new framework to simultaneously detect correspondences among a population of individual subjects, by propagating all manually-placed landmarks from a small set of model images through a dynamically constructed image graph. Specifically, we first establish graph links between models and individual subjects according to pair-wise shape similarity (called as forward step). Next, we detect correspondences for the individual subjects with direct links to any of model images, which is achieved by a new multi-model correspondence detection approach based on our recently-published sparse point matching method. To correct those inaccurate correspondences, we further apply an error detection mechanism to automatically detect wrong correspondences and then update the image graph accordingly (called as backward step). After that, all subject images with detected correspondences are included into the set of model images, and the above two steps of graph expansion and error correction are repeated until accurate correspondences for all subject images are established. Evaluations on real hand X-ray images demonstrate that our proposed method using a dynamic graph construction approach can achieve much higher accuracy and robustness, when compared with the state-of-the-art pair-wise correspondence detection methods as well as a similar method but using static population graph.
Accurate and predictive antibody repertoire profiling by molecular amplification fingerprinting
Khan, Tarik A.; Friedensohn, Simon; de Vries, Arthur R. Gorter; Straszewski, Jakub; Ruscheweyh, Hans-Joachim; Reddy, Sai T.
2016-01-01
High-throughput antibody repertoire sequencing (Ig-seq) provides quantitative molecular information on humoral immunity. However, Ig-seq is compromised by biases and errors introduced during library preparation and sequencing. By using synthetic antibody spike-in genes, we determined that primer bias from multiplex polymerase chain reaction (PCR) library preparation resulted in antibody frequencies with only 42 to 62% accuracy. Additionally, Ig-seq errors resulted in antibody diversity measurements being overestimated by up to 5000-fold. To rectify this, we developed molecular amplification fingerprinting (MAF), which uses unique molecular identifier (UID) tagging before and during multiplex PCR amplification, which enabled tagging of transcripts while accounting for PCR efficiency. Combined with a bioinformatic pipeline, MAF bias correction led to measurements of antibody frequencies with up to 99% accuracy. We also used MAF to correct PCR and sequencing errors, resulting in enhanced accuracy of full-length antibody diversity measurements, achieving 98 to 100% error correction. Using murine MAF-corrected data, we established a quantitative metric of recent clonal expansion—the intraclonal diversity index—which measures the number of unique transcripts associated with an antibody clone. We used this intraclonal diversity index along with antibody frequencies and somatic hypermutation to build a logistic regression model for prediction of the immunological status of clones. The model was able to predict clonal status with high confidence but only when using MAF error and bias corrected Ig-seq data. Improved accuracy by MAF provides the potential to greatly advance Ig-seq and its utility in immunology and biotechnology. PMID:26998518
Accurate simulation dynamics of microscopic filaments using ``caterpillar'' Oseen hydrodynamics
NASA Astrophysics Data System (ADS)
Bailey, A. G.; Lowe, C. P.; Pagonabarraga, I.; Lagomarsino, M. Cosentino
2009-10-01
Microscopic semiflexible filaments suspended in a viscous fluid are widely encountered in biophysical problems. The classic example is the flagella used by microorganisms to generate propulsion. Simulating the dynamics of these filaments numerically is complicated because of the coupling between the motion of the filament and that of the surrounding fluid. An attractive idea is to simplify this coupling by modeling the fluid motion by using Stokeslets distributed at equal intervals along the model filament. We show that, with an appropriate choice of the hydrodynamic radii, one can recover accurate hydrodynamic behavior of a filament with a finite cross section without requiring an explicit surface. This is true, however, only if the hydrodynamic radii take specific values and that they differ in the parallel and perpendicular directions leading to a caterpillarlike hydrodynamic shape. Having demonstrated this, we use the model to compare with analytic theory of filament deformation and rotation in the small deformation limit. Generalization of the methodology, including application to simulations using the Rotne-Prager tensor, is discussed.
State-dependent molecular dynamics.
Yang, Ciann-Dong; Weng, Hung-Jen
2014-01-01
This paper proposes a new mixed quantum mechanics (QM)-molecular mechanics (MM) approach, where MM is replaced by quantum Hamilton mechanics (QHM), which inherits the modeling capability of MM, while preserving the state-dependent nature of QM. QHM, a single mechanics playing the roles of QM and MM simultaneously, will be employed here to derive the three-dimensional quantum dynamics of diatomic molecules. The resulting state-dependent molecular dynamics including vibration, rotation and spin are shown to completely agree with the QM description and well match the experimental vibration-rotation spectrum. QHM can be incorporated into the framework of a mixed quantum-classical Bohmian method to enable a trajectory interpretation of orbital-spin interaction and spin entanglement in molecular dynamics.
Accurate Model Selection of Relaxed Molecular Clocks in Bayesian Phylogenetics
Baele, Guy; Li, Wai Lok Sibon; Drummond, Alexei J.; Suchard, Marc A.; Lemey, Philippe
2013-01-01
Recent implementations of path sampling (PS) and stepping-stone sampling (SS) have been shown to outperform the harmonic mean estimator (HME) and a posterior simulation-based analog of Akaike’s information criterion through Markov chain Monte Carlo (AICM), in Bayesian model selection of demographic and molecular clock models. Almost simultaneously, a Bayesian model averaging approach was developed that avoids conditioning on a single model but averages over a set of relaxed clock models. This approach returns estimates of the posterior probability of each clock model through which one can estimate the Bayes factor in favor of the maximum a posteriori (MAP) clock model; however, this Bayes factor estimate may suffer when the posterior probability of the MAP model approaches 1. Here, we compare these two recent developments with the HME, stabilized/smoothed HME (sHME), and AICM, using both synthetic and empirical data. Our comparison shows reassuringly that MAP identification and its Bayes factor provide similar performance to PS and SS and that these approaches considerably outperform HME, sHME, and AICM in selecting the correct underlying clock model. We also illustrate the importance of using proper priors on a large set of empirical data sets. PMID:23090976
Molecular Dynamics Simulation of Dynamic Response of Beryllium
NASA Astrophysics Data System (ADS)
Thompson, Aidan P.; Lane, J. Matthew D.; Baskes, Michael I.; Desjarlais, Michael P.
2009-06-01
The response of beryllium to dynamic loading has been extensively studied, both experimentally and theoretically, due to its importance in several technological areas. Compared to other metals, it is quite challenging to accurately represent the various anomalous behaviors of beryllium using classical interatomic potentials. The spherically-symmetric EAM potential can not reproduce the observed c/a ratio for α-Be under ambient conditions, which is significantly smaller than the ideal HCP value. The directional-dependence of the MEAM potential overcomes this problem, but introduces additional complexity. We will compare predictions of these classical potentials to experimental measurements of beryllium at ambient conditions, and also to theoretical calculations at high temperatures and pressures. Finally, we will present initial results from non-equilibrium molecular dynamics simulations of beryllium under dynamic loading. This work is supported by the Laboratory Directed Research and Development program at Sandia National Laboratories.
Novel procedures accurately measure drilling mud dynamic filtration
Chenevert, M.E.; Al-Abri, S. ); Jin, L. )
1994-04-25
New equipment and test procedures can determine dynamic mud cake properties such as equilibrium cake thickness, porosity, permeability, compressibility, and erosion resistance. The following were developed to study dynamic filtration: a dynamic filtration cell; a recommended filtration medium; a mud cake thickness device; mud cake porosity determination method; calculation methods for shear rate determination beneath a rotating cone; determination of equilibrium cake thickness, erosion resistance, and compressibility; and preferred filtration display techniques. The article describes the equipment, test procedures, and typical filtration results.
Dynamic fracture toughness determined using molecular dynamics
Swadener, J. G.; Baskes, M. I.; Nastasi, Michael Anthony,
2004-01-01
Molecular dynamics (MD) simulations of fracture in crystalline silicon are conducted in order to determine the dynamic fracture toughness. The MD simulations show how the potential energy released during fracture is partitioned into surface energy, energy stored in defects and kinetic energy. First, the MD fracture simulations are shown to produce brittle fracture and be in reasonable agreement with experimental results. Then dynamic hcture toughness is calculated as the sum of the surface energy and the energy stored as defects directly from the MD models. Models oriented to produce fracture on either (111) or (101) planes are used. For the (101) fracture orientation, equilibrium crack speeds of greater than 80% of the Rayleigh wave speed are obtained. Crack speeds initially show a steep increase with increasing energy release rate followed by a much more gradual increase. No plateau in crack speed is observed for static energy release rates up to 20 J/m{sup 2}. At the point where the change in crack speed behavior occur, the dynamic fracture toughness (J{sub d}) is still within 10% of two times the surface energy (2{gamma}{sub 0}) and changing very slowly. From these MD simulations, it appears that the change in crack speed behavior is due to a change in the kinetic energy generation during dynamic fracture. In addition, MD simulations of facture in silicon with defects were conducted. The addition of defects increases the inelastic dissipation and the energy stored in defects.
Thomas-Fermi molecular dynamics
Clerouin, J.; Pollock, E.L. ); Zerah, G. )
1992-10-15
A three-dimensional density-functional molecular-dynamics code is developed for the Thomas-Fermi density functional as a prototype for density functionals using only the density. Following Car and Parrinello (Phys. Rev. Lett. 55, 2471 (1985)), the electronic density is treated as a dynamical variable. The electronic densities are verified against a multi-ion Thomas-Fermi algorithm due to Parker (Phys. Rev. A 38, 2205 (1988)). As an initial application, the effect of electronic polarization in enhancing ionic diffusion in strongly coupled plasmas is demonstrated.
Available Instruments for Analyzing Molecular Dynamics Trajectories.
Likhachev, I V; Balabaev, N K; Galzitskaya, O V
2016-01-01
Molecular dynamics trajectories are the result of molecular dynamics simulations. Trajectories are sequential snapshots of simulated molecular system which represents atomic coordinates at specific time periods. Based on the definition, in a text format trajectory files are characterized by their simplicity and uselessness. To obtain information from such files, special programs and information processing techniques are applied: from molecular dynamics animation to finding characteristics along the trajectory (versus time). In this review, we describe different programs for processing molecular dynamics trajectories. The performance of these programs, usefulness for analyses of molecular dynamics trajectories, strong and weak aspects are discussed. PMID:27053964
Available Instruments for Analyzing Molecular Dynamics Trajectories
Likhachev, I. V.; Balabaev, N. K.; Galzitskaya, O. V.
2016-01-01
Molecular dynamics trajectories are the result of molecular dynamics simulations. Trajectories are sequential snapshots of simulated molecular system which represents atomic coordinates at specific time periods. Based on the definition, in a text format trajectory files are characterized by their simplicity and uselessness. To obtain information from such files, special programs and information processing techniques are applied: from molecular dynamics animation to finding characteristics along the trajectory (versus time). In this review, we describe different programs for processing molecular dynamics trajectories. The performance of these programs, usefulness for analyses of molecular dynamics trajectories, strong and weak aspects are discussed. PMID:27053964
NMR investigations of molecular dynamics
NASA Astrophysics Data System (ADS)
Palmer, Arthur
2011-03-01
NMR spectroscopy is a powerful experimental approach for characterizing protein conformational dynamics on multiple time scales. The insights obtained from NMR studies are complemented and by molecular dynamics (MD) simulations, which provide full atomistic details of protein dynamics. Homologous mesophilic (E. coli) and thermophilic (T. thermophilus) ribonuclease H (RNase H) enzymes serve to illustrate how changes in protein sequence and structure that affect conformational dynamic processes can be monitored and characterized by joint analysis of NMR spectroscopy and MD simulations. A Gly residue inserted within a putative hinge between helices B and C is conserved among thermophilic RNases H, but absent in mesophilic RNases H. Experimental spin relaxation measurements show that the dynamic properties of T. thermophilus RNase H are recapitulated in E. coli RNase H by insertion of a Gly residue between helices B and C. Additional specific intramolecular interactions that modulate backbone and sidechain dynamical properties of the Gly-rich loop and of the conserved Trp residue flanking the Gly insertion site have been identified using MD simulations and subsequently confirmed by NMR spin relaxation measurements. These results emphasize the importance of hydrogen bonds and local steric interactions in restricting conformational fluctuations, and the absence of such interactions in allowing conformational adaptation to substrate binding.
Numerical methods for molecular dynamics
Skeel, R.D.
1991-01-01
This report summarizes our research progress to date on the use of multigrid methods for three-dimensional elliptic partial differential equations, with particular emphasis on application to the Poisson-Boltzmann equation of molecular biophysics. This research is motivated by the need for fast and accurate numerical solution techniques for three-dimensional problems arising in physics and engineering. In many applications these problems must be solved repeatedly, and the extremely large number of discrete unknowns required to accurately approximate solutions to partial differential equations in three-dimensional regions necessitates the use of efficient solution methods. This situation makes clear the importance of developing methods which are of optimal order (or nearly so), meaning that the number of operations required to solve the discrete problem is on the order of the number of discrete unknowns. Multigrid methods are generally regarded as being in this class of methods, and are in fact provably optimal order for an increasingly large class of problems. The fundamental goal of this research is to develop a fast and accurate numerical technique, based on multi-level principles, for the solutions of the Poisson-Boltzmann equation of molecular biophysics and similar equations occurring in other applications. An outline of the report is as follows. We first present some background material, followed by a survey of the literature on the use of multigrid methods for solving problems similar to the Poisson-Boltzmann equation. A short description of the software we have developed so far is then given, and numerical results are discussed. Finally, our research plans for the coming year are presented.
An Accurate and Dynamic Computer Graphics Muscle Model
NASA Technical Reports Server (NTRS)
Levine, David Asher
1997-01-01
A computer based musculo-skeletal model was developed at the University in the departments of Mechanical and Biomedical Engineering. This model accurately represents human shoulder kinematics. The result of this model is the graphical display of bones moving through an appropriate range of motion based on inputs of EMGs and external forces. The need existed to incorporate a geometric muscle model in the larger musculo-skeletal model. Previous muscle models did not accurately represent muscle geometries, nor did they account for the kinematics of tendons. This thesis covers the creation of a new muscle model for use in the above musculo-skeletal model. This muscle model was based on anatomical data from the Visible Human Project (VHP) cadaver study. Two-dimensional digital images from the VHP were analyzed and reconstructed to recreate the three-dimensional muscle geometries. The recreated geometries were smoothed, reduced, and sliced to form data files defining the surfaces of each muscle. The muscle modeling function opened these files during run-time and recreated the muscle surface. The modeling function applied constant volume limitations to the muscle and constant geometry limitations to the tendons.
Scalable Molecular Dynamics with NAMD
Phillips, James C.; Braun, Rosemary; Wang, Wei; Gumbart, James; Tajkhorshid, Emad; Villa, Elizabeth; Chipot, Christophe; Skeel, Robert D.; Kalé, Laxmikant; Schulten, Klaus
2008-01-01
NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. NAMD scales to hundreds of processors on high-end parallel platforms, as well as tens of processors on low-cost commodity clusters, and also runs on individual desktop and laptop computers. NAMD works with AMBER and CHARMM potential functions, parameters, and file formats. This paper, directed to novices as well as experts, first introduces concepts and methods used in the NAMD program, describing the classical molecular dynamics force field, equations of motion, and integration methods along with the efficient electrostatics evaluation algorithms employed and temperature and pressure controls used. Features for steering the simulation across barriers and for calculating both alchemical and conformational free energy differences are presented. The motivations for and a roadmap to the internal design of NAMD, implemented in C++ and based on Charm++ parallel objects, are outlined. The factors affecting the serial and parallel performance of a simulation are discussed. Next, typical NAMD use is illustrated with representative applications to a small, a medium, and a large biomolecular system, highlighting particular features of NAMD, e.g., the Tcl scripting language. Finally, the paper provides a list of the key features of NAMD and discusses the benefits of combining NAMD with the molecular graphics/sequence analysis software VMD and the grid computing/collaboratory software BioCoRE. NAMD is distributed free of charge with source code at www.ks.uiuc.edu. PMID:16222654
Local Refinements in Classical Molecular Dynamics Simulations
NASA Astrophysics Data System (ADS)
Fackeldey, Konstantin; Weber, Marcus
2014-03-01
Quantum mechanics provide a detailed description of the physical and chemical behavior of molecules. However, with increasing size of the system the complexity rises exponentially, which is prohibitive for efficient dynamical simulation. In contrast, classical molecular dynamics procure a coarser description by using less degrees of freedom. Thus, it seems natural to seek for an adequate trade-off between accurateness and computational feasibility in the simulation of molecules. Here, we propose a novel method, which combines classical molecular simulations with quantum mechanics for molecular systems. For this we decompose the state space of the respective molecule into subsets, by employing a meshfree partition of unity. We show, that this partition allows us to localize an empirical force field and to run locally constrained classical trajectories. Within each subset, we compute the energy on the quantum level for a fixed number of spatial states (ab initio points). With these energy values from the ab initio points we have a local scattered data problem, which can be solved by the moving least squares method.
Accurate direct Eulerian simulation of dynamic elastic-plastic flow
Kamm, James R; Walter, John W
2009-01-01
The simulation of dynamic, large strain deformation is an important, difficult, and unsolved computational challenge. Existing Eulerian schemes for dynamic material response are plagued by unresolved issues. We present a new scheme for the first-order system of elasto-plasticity equations in the Eulerian frame. This system has an intrinsic constraint on the inverse deformation gradient. Standard Godunov schemes do not satisfy this constraint. The method of Flux Distributions (FD) was devised to discretely enforce such constraints for numerical schemes with cell-centered variables. We describe a Flux Distribution approach that enforces the inverse deformation gradient constraint. As this approach is new and novel, we do not yet have numerical results to validate our claims. This paper is the first installment of our program to develop this new method.
Better, Cheaper, Faster Molecular Dynamics
NASA Technical Reports Server (NTRS)
Pohorille, Andrew; DeVincenzi, Donald L. (Technical Monitor)
2001-01-01
Recent, revolutionary progress in genomics and structural, molecular and cellular biology has created new opportunities for molecular-level computer simulations of biological systems by providing vast amounts of data that require interpretation. These opportunities are further enhanced by the increasing availability of massively parallel computers. For many problems, the method of choice is classical molecular dynamics (iterative solving of Newton's equations of motion). It focuses on two main objectives. One is to calculate the relative stability of different states of the system. A typical problem that has' such an objective is computer-aided drug design. Another common objective is to describe evolution of the system towards a low energy (possibly the global minimum energy), "native" state. Perhaps the best example of such a problem is protein folding. Both types of problems share the same difficulty. Often, different states of the system are separated by high energy barriers, which implies that transitions between these states are rare events. This, in turn, can greatly impede exploration of phase space. In some instances this can lead to "quasi non-ergodicity", whereby a part of phase space is inaccessible on time scales of the simulation. To overcome this difficulty and to extend molecular dynamics to "biological" time scales (millisecond or longer) new physical formulations and new algorithmic developments are required. To be efficient they should account for natural limitations of multi-processor computer architecture. I will present work along these lines done in my group. In particular, I will focus on a new approach to calculating the free energies (stability) of different states and to overcoming "the curse of rare events". I will also discuss algorithmic improvements to multiple time step methods and to the treatment of slowly decaying, log-ranged, electrostatic effects.
Molecular dynamics of polymer growth
NASA Astrophysics Data System (ADS)
Akkermans, Reinier L. C.; Toxvaerd, Søren; Briels, W. J.
1998-08-01
The irreversible polymerization of a monomer liquid has been studied by molecular-dynamics simulation in two and three dimensions. The growth process is studied under good solvent conditions in the dilute regime and up to semidilute and concentrated regimes. In the dilute regime we observe a reaction limitation due to trapping of the growing centers, which is more pronounced in the lower dimension. At higher concentrations the presence of other chains decreases the monomer mobility and reaction rate. Conformational properties are studied by scaling analysis of end-to-end and gyration radii. A crossover from swollen conformations towards screened conformations is observed as growth proceeds.
Dynamic pseudos: How accurate outside their parent case?
Ekrann, S.; Mykkeltveit, J.
1995-12-31
If properly constructed, dynamic pseudos allow the parent solution from which they were derived to be exactly reproduced, in a certain well-defined sense, in a subsequent coarse grid simulation. The paper reports extensive numerical experimentation, in 1D homogeneous and heterogeneous media, to determine the performance of pseudos when used outside their parent case. The authors perturb fluid viscosities and injection rate, as well as realization. Parent solutions are produced analytically, via a generalization of the Buckley-Leverett technique, as are true solutions in off-parent cases. Capillarity is neglected in these experiments, while gravity is sometimes retained in order to force rate sensitivity.
Accurate boundary conditions for exterior problems in gas dynamics
NASA Technical Reports Server (NTRS)
Hagstrom, Thomas; Hariharan, S. I.
1988-01-01
The numerical solution of exterior problems is typically accomplished by introducing an artificial, far field boundary and solving the equations on a truncated domain. For hyperbolic systems, boundary conditions at this boundary are often derived by imposing a principle of no reflection. However, waves with spherical symmetry in gas dynamics satisfy equations where incoming and outgoing Riemann variables are coupled. This suggests that natural reflections may be important. A reflecting boundary condition is proposed based on an asymptotic solution of the far field equations. Nonlinear energy estimates are obtained for the truncated problem and numerical experiments presented to validate the theory.
Accurate boundary conditions for exterior problems in gas dynamics
NASA Technical Reports Server (NTRS)
Hagstrom, Thomas; Hariharan, S. I.
1988-01-01
The numerical solution of exterior problems is typically accomplished by introducing an artificial, far-field boundary and solving the equations on a truncated domain. For hyperbolic systems, boundary conditions at this boundary are often derived by imposing a principle of no reflection. However, waves with spherical symmetry in gas dynamics satisfy equations where incoming and outgoing Riemann variables are coupled. This suggests that natural reflections may be important. A reflecting boundary condition is proposed based on an asymptotic solution of the far-field equations. Nonlinear energy estimates are obtained for the truncated problem and numerical experiments presented to validate the theory.
Radiation in molecular dynamic simulations
Glosli, J; Graziani, F; More, R; Murillo, M; Streitz, F; Surh, M
2008-10-13
Hot dense radiative (HDR) plasmas common to Inertial Confinement Fusion (ICF) and stellar interiors have high temperature (a few hundred eV to tens of keV), high density (tens to hundreds of g/cc) and high pressure (hundreds of Megabars to thousands of Gigabars). Typically, such plasmas undergo collisional, radiative, atomic and possibly thermonuclear processes. In order to describe HDR plasmas, computational physicists in ICF and astrophysics use atomic-scale microphysical models implemented in various simulation codes. Experimental validation of the models used to describe HDR plasmas are difficult to perform. Direct Numerical Simulation (DNS) of the many-body interactions of plasmas is a promising approach to model validation but, previous work either relies on the collisionless approximation or ignores radiation. We present a new numerical simulation technique to address a currently unsolved problem: the extension of molecular dynamics to collisional plasmas including emission and absorption of radiation. The new technique passes a key test: it relaxes to a blackbody spectrum for a plasma in local thermodynamic equilibrium. This new tool also provides a method for assessing the accuracy of energy and momentum exchange models in hot dense plasmas. As an example, we simulate the evolution of non-equilibrium electron, ion, and radiation temperatures for a hydrogen plasma using the new molecular dynamics simulation capability.
Molecular dynamics of interface rupture
NASA Technical Reports Server (NTRS)
Koplik, Joel; Banavar, Jayanth R.
1993-01-01
Several situations have been studied in which a fluid-vapor or fluid-fluid interface ruptures, using molecular dynamics simulations of 3000 to 20,000 Lennard-Jones molecules in three dimensions. The cases studied are the Rayleigh instability of a liquid thread, the burst of a liquid drop immersed in a second liquid undergoing shear, and the rupture of a liquid sheet in an extensional flow. The late stages of the rupture process involve the gradual withdrawal of molecules from a thinning neck, or the appearance and growth of holes in a sheet. In all cases, it is found that despite the small size of the systems studied, tens of angstroms, the dynamics is in at least qualitative accord with the behavior expected from continuum calculations, and in some cases the agreement is to within tens of percent. Remarkably, this agreement occurs even though the Eulerian velocity and stress fields are essentially unmeasurable - dominated by thermal noise. The limitations and prospects for such molecular simulation techniques are assessed.
A concurrent multiscale micromorphic molecular dynamics
Li, Shaofan Tong, Qi
2015-04-21
In this work, we have derived a multiscale micromorphic molecular dynamics (MMMD) from first principle to extend the (Andersen)-Parrinello-Rahman molecular dynamics to mesoscale and continuum scale. The multiscale micromorphic molecular dynamics is a con-current three-scale dynamics that couples a fine scale molecular dynamics, a mesoscale micromorphic dynamics, and a macroscale nonlocal particle dynamics together. By choosing proper statistical closure conditions, we have shown that the original Andersen-Parrinello-Rahman molecular dynamics is the homogeneous and equilibrium case of the proposed multiscale micromorphic molecular dynamics. In specific, we have shown that the Andersen-Parrinello-Rahman molecular dynamics can be rigorously formulated and justified from first principle, and its general inhomogeneous case, i.e., the three scale con-current multiscale micromorphic molecular dynamics can take into account of macroscale continuum mechanics boundary condition without the limitation of atomistic boundary condition or periodic boundary conditions. The discovered multiscale scale structure and the corresponding multiscale dynamics reveal a seamless transition from atomistic scale to continuum scale and the intrinsic coupling mechanism among them based on first principle formulation.
Shear flow by molecular dynamics
NASA Astrophysics Data System (ADS)
Heyes, D. M.
1985-08-01
A detailed comparison is made between a number of methods for generating shear flow in Molecular Dynamics computer simulation. Algorithms which closely mimic most experimental methods for producing shear flow are those by Trozzi and Ciccotti, and Ashurst and Hoover. They employ hard wall boundaries and fluid walls respectively (with sheared cell periodicity being only in two dimensions). The sheared fluid properties are therefore inextricably linked with interfacial effects. These problems are largely eliminated by the Lees and Edwards scheme which creates a pseudo-infinite sheared material. There are a number of derivatives of this model including one favoured by the author for investigating non-linear viscoelastic phenomena. A number of results from this scheme pertaining to the Lennard-Jones liquid are presented.
Buckybomb: Reactive Molecular Dynamics Simulation.
Chaban, Vitaly V; Fileti, Eudes Eterno; Prezhdo, Oleg V
2015-03-01
Energetic materials, such as explosives, propellants, and pyrotechnics, are widely used in civilian and military applications. Nanoscale explosives represent a special group because of the high density of energetic covalent bonds. The reactive molecular dynamics (ReaxFF) study of nitrofullerene decomposition reported here provides a detailed chemical mechanism of explosion of a nanoscale carbon material. Upon initial heating, C60(NO2)12 disintegrates, increasing temperature and pressure by thousands of Kelvins and bars within tens of picoseconds. The explosion starts with NO2 group isomerization into C-O-N-O, followed by emission of NO molecules and formation of CO groups on the buckyball surface. NO oxidizes into NO2, and C60 falls apart, liberating CO2. At the highest temperatures, CO2 gives rise to diatomic carbon. The study shows that the initiation temperature and released energy depend strongly on the chemical composition and density of the material. PMID:26262672
Emergent Phenomena via Molecular Dynamics
NASA Astrophysics Data System (ADS)
Rapaport, D. C.
Emergent phenomena are unusual because they are not obvious consequences of the design of the systems in which they appear, a feature no less relevant when they are being simulated. Several systems that exhibit surprisingly rich emergent behavior, each studied by molecular dynamics (MD) simulation, are described: (i) Modeling self-assembly processes associated with virus growth reveals the ability to achieve error-free assembly, where paradoxically, near-maximum yields are due to reversible bond formation. (ii) In fluids studied at the atomistic level, complex hydrodynamic phenomena in rotating and convecting fluids - the Taylor- Couette and Rayleigh-Bénard instabilities - can be reproduced, despite the limited length and time scales accessible by MD. (iii) Segregation studies of granular mixtures in a rotating drum reproduce the expected, but counterintuitive, axial and radial segregation, while for the case of a vertically vibrated layer a novel form of horizontal segregation is revealed.
Buckybomb: Reactive Molecular Dynamics Simulation.
Chaban, Vitaly V; Fileti, Eudes Eterno; Prezhdo, Oleg V
2015-03-01
Energetic materials, such as explosives, propellants, and pyrotechnics, are widely used in civilian and military applications. Nanoscale explosives represent a special group because of the high density of energetic covalent bonds. The reactive molecular dynamics (ReaxFF) study of nitrofullerene decomposition reported here provides a detailed chemical mechanism of explosion of a nanoscale carbon material. Upon initial heating, C60(NO2)12 disintegrates, increasing temperature and pressure by thousands of Kelvins and bars within tens of picoseconds. The explosion starts with NO2 group isomerization into C-O-N-O, followed by emission of NO molecules and formation of CO groups on the buckyball surface. NO oxidizes into NO2, and C60 falls apart, liberating CO2. At the highest temperatures, CO2 gives rise to diatomic carbon. The study shows that the initiation temperature and released energy depend strongly on the chemical composition and density of the material.
Sezen, Melda; Register, Jeffrey T; Yao, Yao; Glisic, Branko; Loo, Yueh-Lin
2016-06-01
The polarity and the magnitude of polyaniline's gauge factor are tuned through structural modification. Combining conducting polymers with gauge factors of opposite polarities yields an accurate temperature sensor, even when deployed under dynamic strains. PMID:27061270
Molecular dynamics of membrane proteins.
Woolf, Thomas B.; Crozier, Paul Stewart; Stevens, Mark Jackson
2004-10-01
Understanding the dynamics of the membrane protein rhodopsin will have broad implications for other membrane proteins and cellular signaling processes. Rhodopsin (Rho) is a light activated G-protein coupled receptor (GPCR). When activated by ligands, GPCRs bind and activate G-proteins residing within the cell and begin a signaling cascade that results in the cell's response to external stimuli. More than 50% of all current drugs are targeted toward G-proteins. Rho is the prototypical member of the class A GPCR superfamily. Understanding the activation of Rho and its interaction with its Gprotein can therefore lead to a wider understanding of the mechanisms of GPCR activation and G-protein activation. Understanding the dark to light transition of Rho is fully analogous to the general ligand binding and activation problem for GPCRs. This transition is dependent on the lipid environment. The effect of lipids on membrane protein activity in general has had little attention, but evidence is beginning to show a significant role for lipids in membrane protein activity. Using the LAMMPS program and simulation methods benchmarked under the IBIG program, we perform a variety of allatom molecular dynamics simulations of membrane proteins.
Dynamical Localization in Molecular Systems.
NASA Astrophysics Data System (ADS)
Wang, Xidi
In the first four chapters of this thesis we concentrate on the Davydov model which describes the vibrational energy quanta of Amide I bonds (C=O bonds on the alpha -helix) coupled to the acoustic phonon modes of the alpha-helix backbone in the form of a Frohlich Hamiltonian. Following a brief introduction in chapter one, in chapter two we formulate the dynamics of vibrational quanta at finite temperature by using coherent state products. The fluctuation-dissipation relation is derived. At zero temperature, in the continuum limit, we recover the original results of Davydov. We also achieve good agreement with numerical simulations. In chapter three, the net contraction of the lattice is calculated exactly at any temperature, and its relation to the so -call "topological stability" of the Davydov soliton is discussed. In the second section of the chapter three we calculate the overtone spectra of crystalline acetanilide (according to some opinions ACN provides experimental evidence for the existence of Davydov solitons). Good agreement with experimental data has been obtained. In chapter four we study the self-trapped vibrational excitations by the Quantum Monte Carlo technique. For a single excitation, the temperature dependence of different physical observables is calculated. The quasi-particle which resembles the Davydov soliton has been found to be fairly narrow using the most commonly used data for the alpha -helix; at temperatures above a few Kelvin, the quasi-particle reaches its smallest limit (extends over three sites), which implies diffusive motion of the small polaron-like quasi-particle at high temperatures. For the multi-excitation case, bound pairs and clusters of excitations are found at low temperatures; they gradually dissociate when the temperature of the system is increased as calculated from the density-density correlation function. In the last chapter of this thesis, we study a more general model of dynamical local modes in molecular systems
NASA Astrophysics Data System (ADS)
Barone, Luciano Maria; Simonazzi, Riccardo; Tenenbaum, Alexander
1995-09-01
We have studied portability, efficiency and accuracy of a standard Molecular Dynamics simulation on the SIMD parallel computer APE100. Computing speed performance and physical system size range have been analyzed and compared with those of a conventional computer. Short range and long range potentials have been considered, and the comparative advantage of different simulation approaches has been assessed. For long range potentials, APE turns out to be faster than a conventional computer; large systems can be conveniently simulated using either the cloning approach (up to ˜ 10 5 particles) or a domain decomposition with the systolic method. In the case of short range potentials and systems with diffusion (like a liquid), APE is convenient only when using a large number of processors. In a special case (a crystal without diffusion), a specific domain decomposition technique with frames makes APE advantageous for intermediate and large systems. Using the latter technique we have studied in detail the effect of different numerical error sources, and compared the accuracy of APE with that of a conventional computer.
Parametrizing linear generalized Langevin dynamics from explicit molecular dynamics simulations
Gottwald, Fabian; Karsten, Sven; Ivanov, Sergei D. Kühn, Oliver
2015-06-28
Fundamental understanding of complex dynamics in many-particle systems on the atomistic level is of utmost importance. Often the systems of interest are of macroscopic size but can be partitioned into a few important degrees of freedom which are treated most accurately and others which constitute a thermal bath. Particular attention in this respect attracts the linear generalized Langevin equation, which can be rigorously derived by means of a linear projection technique. Within this framework, a complicated interaction with the bath can be reduced to a single memory kernel. This memory kernel in turn is parametrized for a particular system studied, usually by means of time-domain methods based on explicit molecular dynamics data. Here, we discuss that this task is more naturally achieved in frequency domain and develop a Fourier-based parametrization method that outperforms its time-domain analogues. Very surprisingly, the widely used rigid bond method turns out to be inappropriate in general. Importantly, we show that the rigid bond approach leads to a systematic overestimation of relaxation times, unless the system under study consists of a harmonic bath bi-linearly coupled to the relevant degrees of freedom.
Hele, Timothy J H; Willatt, Michael J; Muolo, Andrea; Althorpe, Stuart C
2015-05-21
We recently obtained a quantum-Boltzmann-conserving classical dynamics by making a single change to the derivation of the "Classical Wigner" approximation. Here, we show that the further approximation of this "Matsubara dynamics" gives rise to two popular heuristic methods for treating quantum Boltzmann time-correlation functions: centroid molecular dynamics (CMD) and ring-polymer molecular dynamics (RPMD). We show that CMD is a mean-field approximation to Matsubara dynamics, obtained by discarding (classical) fluctuations around the centroid, and that RPMD is the result of discarding a term in the Matsubara Liouvillian which shifts the frequencies of these fluctuations. These findings are consistent with previous numerical results and give explicit formulae for the terms that CMD and RPMD leave out.
Hansen, Katja; Biegler, Franziska; Ramakrishnan, Raghunathan; Pronobis, Wiktor; von Lilienfeld, O Anatole; Müller, Klaus-Robert; Tkatchenko, Alexandre
2015-06-18
Simultaneously accurate and efficient prediction of molecular properties throughout chemical compound space is a critical ingredient toward rational compound design in chemical and pharmaceutical industries. Aiming toward this goal, we develop and apply a systematic hierarchy of efficient empirical methods to estimate atomization and total energies of molecules. These methods range from a simple sum over atoms, to addition of bond energies, to pairwise interatomic force fields, reaching to the more sophisticated machine learning approaches that are capable of describing collective interactions between many atoms or bonds. In the case of equilibrium molecular geometries, even simple pairwise force fields demonstrate prediction accuracy comparable to benchmark energies calculated using density functional theory with hybrid exchange-correlation functionals; however, accounting for the collective many-body interactions proves to be essential for approaching the “holy grail” of chemical accuracy of 1 kcal/mol for both equilibrium and out-of-equilibrium geometries. This remarkable accuracy is achieved by a vectorized representation of molecules (so-called Bag of Bonds model) that exhibits strong nonlocality in chemical space. In addition, the same representation allows us to predict accurate electronic properties of molecules, such as their polarizability and molecular frontier orbital energies.
Hansen, Katja; Biegler, Franziska; Ramakrishnan, Raghunathan; Pronobis, Wiktor; von Lilienfeld, O. Anatole; Müller, Klaus -Robert; Tkatchenko, Alexandre
2015-06-04
Simultaneously accurate and efficient prediction of molecular properties throughout chemical compound space is a critical ingredient toward rational compound design in chemical and pharmaceutical industries. Aiming toward this goal, we develop and apply a systematic hierarchy of efficient empirical methods to estimate atomization and total energies of molecules. These methods range from a simple sum over atoms, to addition of bond energies, to pairwise interatomic force fields, reaching to the more sophisticated machine learning approaches that are capable of describing collective interactions between many atoms or bonds. In the case of equilibrium molecular geometries, even simple pairwise force fields demonstrate prediction accuracy comparable to benchmark energies calculated using density functional theory with hybrid exchange-correlation functionals; however, accounting for the collective many-body interactions proves to be essential for approaching the “holy grail” of chemical accuracy of 1 kcal/mol for both equilibrium and out-of-equilibrium geometries. This remarkable accuracy is achieved by a vectorized representation of molecules (so-called Bag of Bonds model) that exhibits strong nonlocality in chemical space. The same representation allows us to predict accurate electronic properties of molecules, such as their polarizability and molecular frontier orbital energies.
Hansen, Katja; Biegler, Franziska; Ramakrishnan, Raghunathan; Pronobis, Wiktor; von Lilienfeld, O. Anatole; Müller, Klaus -Robert; Tkatchenko, Alexandre
2015-06-04
Simultaneously accurate and efficient prediction of molecular properties throughout chemical compound space is a critical ingredient toward rational compound design in chemical and pharmaceutical industries. Aiming toward this goal, we develop and apply a systematic hierarchy of efficient empirical methods to estimate atomization and total energies of molecules. These methods range from a simple sum over atoms, to addition of bond energies, to pairwise interatomic force fields, reaching to the more sophisticated machine learning approaches that are capable of describing collective interactions between many atoms or bonds. In the case of equilibrium molecular geometries, even simple pairwise force fields demonstratemore » prediction accuracy comparable to benchmark energies calculated using density functional theory with hybrid exchange-correlation functionals; however, accounting for the collective many-body interactions proves to be essential for approaching the “holy grail” of chemical accuracy of 1 kcal/mol for both equilibrium and out-of-equilibrium geometries. This remarkable accuracy is achieved by a vectorized representation of molecules (so-called Bag of Bonds model) that exhibits strong nonlocality in chemical space. The same representation allows us to predict accurate electronic properties of molecules, such as their polarizability and molecular frontier orbital energies.« less
2015-01-01
Simultaneously accurate and efficient prediction of molecular properties throughout chemical compound space is a critical ingredient toward rational compound design in chemical and pharmaceutical industries. Aiming toward this goal, we develop and apply a systematic hierarchy of efficient empirical methods to estimate atomization and total energies of molecules. These methods range from a simple sum over atoms, to addition of bond energies, to pairwise interatomic force fields, reaching to the more sophisticated machine learning approaches that are capable of describing collective interactions between many atoms or bonds. In the case of equilibrium molecular geometries, even simple pairwise force fields demonstrate prediction accuracy comparable to benchmark energies calculated using density functional theory with hybrid exchange-correlation functionals; however, accounting for the collective many-body interactions proves to be essential for approaching the “holy grail” of chemical accuracy of 1 kcal/mol for both equilibrium and out-of-equilibrium geometries. This remarkable accuracy is achieved by a vectorized representation of molecules (so-called Bag of Bonds model) that exhibits strong nonlocality in chemical space. In addition, the same representation allows us to predict accurate electronic properties of molecules, such as their polarizability and molecular frontier orbital energies. PMID:26113956
Time-Dependent Molecular Reaction Dynamics
NASA Astrophysics Data System (ADS)
Öhrn, Yngve
2007-11-01
This paper is a brief review of a time-dependent, direct, nonadiabatic theory of molecular processes called Electron Nuclear Dynamics (END). This approach to the study of molecular reaction dynamics is a hierarchical theory that can be applied at various levels of approximation. The simplest level of END uses classical nuclei and represents all electrons by a single, complex, determinantal wave function. The wave function parameters such as average nuclear positions and momenta, and molecular orbital coefcients carry the time dependence and serve as dynamical variables. Examples of application are given of the simplest level of END to ion-atom and ion-molecule reactions.
Shaughnessy, M C; Jones, R E
2016-02-01
We develop and demonstrate a method to efficiently use density functional calculations to drive classical dynamics of complex atomic and molecular systems. The method has the potential to scale to systems and time scales unreachable with current ab initio molecular dynamics schemes. It relies on an adapting dataset of independently computed Hellmann-Feynman forces for atomic configurations endowed with a distance metric. The metric on configurations enables fast database lookup and robust interpolation of the stored forces. We discuss mechanisms for the database to adapt to the needs of the evolving dynamics, while maintaining accuracy, and other extensions of the basic algorithm.
Shaughnessy, M C; Jones, R E
2016-02-01
We develop and demonstrate a method to efficiently use density functional calculations to drive classical dynamics of complex atomic and molecular systems. The method has the potential to scale to systems and time scales unreachable with current ab initio molecular dynamics schemes. It relies on an adapting dataset of independently computed Hellmann-Feynman forces for atomic configurations endowed with a distance metric. The metric on configurations enables fast database lookup and robust interpolation of the stored forces. We discuss mechanisms for the database to adapt to the needs of the evolving dynamics, while maintaining accuracy, and other extensions of the basic algorithm. PMID:26669825
Hele, Timothy J. H.; Willatt, Michael J.; Muolo, Andrea; Althorpe, Stuart C.
2015-05-21
We recently obtained a quantum-Boltzmann-conserving classical dynamics by making a single change to the derivation of the “Classical Wigner” approximation. Here, we show that the further approximation of this “Matsubara dynamics” gives rise to two popular heuristic methods for treating quantum Boltzmann time-correlation functions: centroid molecular dynamics (CMD) and ring-polymer molecular dynamics (RPMD). We show that CMD is a mean-field approximation to Matsubara dynamics, obtained by discarding (classical) fluctuations around the centroid, and that RPMD is the result of discarding a term in the Matsubara Liouvillian which shifts the frequencies of these fluctuations. These findings are consistent with previous numerical results and give explicit formulae for the terms that CMD and RPMD leave out.
Molecular ions, Rydberg spectroscopy and dynamics
Jungen, Ch.
2015-01-22
Ion spectroscopy, Rydberg spectroscopy and molecular dynamics are closely related subjects. Multichannel quantum defect theory is a theoretical approach which draws on this close relationship and thereby becomes a powerful tool for the study of systems consisting of a positively charged molecular ion core interacting with an electron which may be loosely bound or freely scattering.
Modeling the Hydrogen Bond within Molecular Dynamics
ERIC Educational Resources Information Center
Lykos, Peter
2004-01-01
The structure of a hydrogen bond is elucidated within the framework of molecular dynamics based on the model of Rahman and Stillinger (R-S) liquid water treatment. Thus, undergraduates are exposed to the powerful but simple use of classical mechanics to solid objects from a molecular viewpoint.
Protein dynamics: Moore's law in molecular biology.
Vendruscolo, Michele; Dobson, Christopher M
2011-01-25
The millisecond barrier has been broken in molecular dynamics simulations of proteins. Such simulations are increasingly revealing the inner workings of biological systems by generating atomic-level descriptions of their behaviour that make testable predictions about key molecular processes.
Molecular Dynamics Simulations of Simple Liquids
ERIC Educational Resources Information Center
Speer, Owner F.; Wengerter, Brian C.; Taylor, Ramona S.
2004-01-01
An experiment, in which students were given the opportunity to perform molecular dynamics simulations on a series of molecular liquids using the Amber suite of programs, is presented. They were introduced to both physical theories underlying classical mechanics simulations and to the atom-atom pair distribution function.
Parallel Molecular Dynamics Program for Molecules
Plimpton, Steve
1995-03-07
ParBond is a parallel classical molecular dynamics code that models bonded molecular systems, typically of an organic nature. It uses classical force fields for both non-bonded Coulombic and Van der Waals interactions and for 2-, 3-, and 4-body bonded (bond, angle, dihedral, and improper) interactions. It integrates Newton''s equation of motion for the molecular system and evaluates various thermodynamical properties of the system as it progresses.
NASA Astrophysics Data System (ADS)
Sellers, Michael; Lisal, Martin; Brennan, John
2015-06-01
Investigating the ability of a molecular model to accurately represent a real material is crucial to model development and use. When the model simulates materials in extreme conditions, one such property worth evaluating is the phase transition point. However, phase transitions are often overlooked or approximated because of difficulty or inaccuracy when simulating them. Techniques such as super-heating or super-squeezing a material to induce a phase change suffer from inherent timescale limitations leading to ``over-driving,'' and dual-phase simulations require many long-time runs to seek out what frequently results in an inexact location of phase-coexistence. We present a compilation of methods for the determination of solid-solid and solid-liquid phase transition points through the accurate calculation of the chemical potential. The methods are applied to the Smith-Bharadwaj atomistic potential's representation of cyclotrimethylene trinitramine (RDX) to accurately determine its melting point (Tm) and the alpha to gamma solid phase transition pressure. We also determine Tm for a coarse-grain model of RDX, and compare its value to experiment and atomistic counterpart. All methods are employed via the LAMMPS simulator, resulting in 60-70 simulations that total 30-50 ns. Approved for public release. Distribution is unlimited.
Ab initio molecular dynamics: Concepts, recent developments, and future trends
Iftimie, Radu; Minary, Peter; Tuckerman, Mark E.
2005-01-01
The methodology of ab initio molecular dynamics, wherein finite-temperature dynamical trajectories are generated by using forces computed “on the fly” from electronic structure calculations, has had a profound influence in modern theoretical research. Ab initio molecular dynamics allows chemical processes in condensed phases to be studied in an accurate and unbiased manner, leading to new paradigms in the elucidation of microscopic mechanisms, rationalization of experimental data, and testable predictions of new phenomena. The purpose of this work is to give a brief introduction to the technique and to review several important recent developments in the field. Several illustrative examples showing the power of the technique have been chosen. Perspectives on future directions in the field also will be given. PMID:15870204
A large catalog of accurate distances to molecular clouds from PS1 photometry
Schlafly, E. F.; Rix, H.-W.; Martin, N. F.; Green, G.; Finkbeiner, D. P.; Bell, E. F.; Burgett, W. S.; Chambers, K. C.; Hodapp, K. W.; Kaiser, N.; Magnier, E. A.; Tonry, J. L.; Draper, P. W.; Metcalfe, N.; Price, P. A.
2014-05-01
Distance measurements to molecular clouds are important but are often made separately for each cloud of interest, employing very different data and techniques. We present a large, homogeneous catalog of distances to molecular clouds, most of which are of unprecedented accuracy. We determine distances using optical photometry of stars along lines of sight toward these clouds, obtained from PanSTARRS-1. We simultaneously infer the reddenings and distances to these stars, tracking the full probability distribution function using a technique presented in Green et al. We fit these star-by-star measurements using a simple dust screen model to find the distance to each cloud. We thus estimate the distances to almost all of the clouds in the Magnani et al. catalog, as well as many other well-studied clouds, including Orion, Perseus, Taurus, Cepheus, Polaris, California, and Monoceros R2, avoiding only the inner Galaxy. Typical statistical uncertainties in the distances are 5%, though the systematic uncertainty stemming from the quality of our stellar models is about 10%. The resulting catalog is the largest catalog of accurate, directly measured distances to molecular clouds. Our distance estimates are generally consistent with available distance estimates from the literature, though in some cases the literature estimates are off by a factor of more than two.
NASA Astrophysics Data System (ADS)
Mills, Andrew A.; Ford, Kyle B.; Kreckel, Holger; Perera, Manori; Crabtree, Kyle N.; McCall, Benjamin J.
2009-06-01
With the advent of Herschel and SOFIA, laboratory methods capable of providing molecular rest frequencies in the terahertz and sub-millimeter regime are increasingly important. As of yet, it has been difficult to perform spectroscopy in this wavelength region due to the limited availability of radiation sources, optics, and detectors. Our goal is to provide accurate THz rest frequencies for molecular ions by combining previously recorded microwave transitions with combination differences obtained from high precision mid-IR spectroscopy. We are constructing a Sensitive Resolved Ion Beam Spectroscopy setup which will harness the benefits of kinematic compression in a molecular ion beam to enable very high resolution spectroscopy. This ion beam is interrogated by continuous-wave cavity ringdown spectroscopy using a home-made widely tunable difference frequency laser that utilizes two near-IR lasers and a periodically-poled lithium niobate crystal. Here, we report our efforts to optimize our ion beam spectrometer and to perform high-precision and high-accuracy frequency measurements using an optical frequency comb. footnote
Dynamic molecular crystals with switchable physical properties.
Sato, Osamu
2016-06-21
The development of molecular materials whose physical properties can be controlled by external stimuli - such as light, electric field, temperature, and pressure - has recently attracted much attention owing to their potential applications in molecular devices. There are a number of ways to alter the physical properties of crystalline materials. These include the modulation of the spin and redox states of the crystal's components, or the incorporation within the crystalline lattice of tunable molecules that exhibit stimuli-induced changes in their molecular structure. A switching behaviour can also be induced by changing the molecular orientation of the crystal's components, even in cases where the overall molecular structure is not affected. Controlling intermolecular interactions within a molecular material is also an effective tool to modulate its physical properties. This Review discusses recent advances in the development of such stimuli-responsive, switchable crystalline compounds - referred to here as dynamic molecular crystals - and suggests how different approaches can serve to prepare functional materials. PMID:27325090
Molecular dynamics simulations: advances and applications
Hospital, Adam; Goñi, Josep Ramon; Orozco, Modesto; Gelpí, Josep L
2015-01-01
Molecular dynamics simulations have evolved into a mature technique that can be used effectively to understand macromolecular structure-to-function relationships. Present simulation times are close to biologically relevant ones. Information gathered about the dynamic properties of macromolecules is rich enough to shift the usual paradigm of structural bioinformatics from studying single structures to analyze conformational ensembles. Here, we describe the foundations of molecular dynamics and the improvements made in the direction of getting such ensemble. Specific application of the technique to three main issues (allosteric regulation, docking, and structure refinement) is discussed. PMID:26604800
Molecular dynamics simulations: advances and applications
Hospital, Adam; Goñi, Josep Ramon; Orozco, Modesto; Gelpí, Josep L
2015-01-01
Molecular dynamics simulations have evolved into a mature technique that can be used effectively to understand macromolecular structure-to-function relationships. Present simulation times are close to biologically relevant ones. Information gathered about the dynamic properties of macromolecules is rich enough to shift the usual paradigm of structural bioinformatics from studying single structures to analyze conformational ensembles. Here, we describe the foundations of molecular dynamics and the improvements made in the direction of getting such ensemble. Specific application of the technique to three main issues (allosteric regulation, docking, and structure refinement) is discussed.
Molecular dynamics simulations of large macromolecular complexes
Perilla, Juan R.; Goh, Boon Chong; Cassidy, C. Keith; Liu, Bo; Bernardi, Rafael C.; Rudack, Till; Yu, Hang; Wu, Zhe; Schulten, Klaus
2015-01-01
Connecting dynamics to structural data from diverse experimental sources, molecular dynamics simulations permit the exploration of biological phenomena in unparalleled detail. Advances in simulations are moving the atomic resolution descriptions of biological systems into the million-to-billion atom regime, in which numerous cell functions reside. In this opinion, we review the progress, driven by large-scale molecular dynamics simulations, in the study of viruses, ribosomes, bioenergetic systems, and other diverse applications. These examples highlight the utility of molecular dynamics simulations in the critical task of relating atomic detail to the function of supramolecular complexes, a task that cannot be achieved by smaller-scale simulations or existing experimental approaches alone. PMID:25845770
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.
Spinelli, Orietta; Rambaldi, Alessandro; Rigo, Francesca; Zanghì, Pamela; D'Agostini, Elena; Amicarelli, Giulia; Colotta, Francesco; Divona, Mariadomenica; Ciardi, Claudia; Coco, Francesco Lo; Minnucci, Giulia
2015-01-01
The diagnostic work-up of acute promyelocytic leukemia (APL) includes the cytogenetic demonstration of the t(15;17) translocation and/or the PML-RARA chimeric transcript by RQ-PCR or RT-PCR. This latter assays provide suitable results in 3-6 hours. We describe here two new, rapid and specific assays that detect PML-RARA transcripts, based on the RT-QLAMP (Reverse Transcription-Quenching Loop-mediated Isothermal Amplification) technology in which RNA retrotranscription and cDNA amplification are carried out in a single tube with one enzyme at one temperature, in fluorescence and real time format. A single tube triplex assay detects bcr1 and bcr3 PML-RARA transcripts along with GUS housekeeping gene. A single tube duplex assay detects bcr2 and GUSB. In 73 APL cases, these assays detected in 16 minutes bcr1, bcr2 and bcr3 transcripts. All 81 non-APL samples were negative by RT-QLAMP for chimeric transcripts whereas GUSB was detectable. In 11 APL patients in which RT-PCR yielded equivocal breakpoint type results, RT-QLAMP assays unequivocally and accurately defined the breakpoint type (as confirmed by sequencing). Furthermore, RT-QLAMP could amplify two bcr2 transcripts with particularly extended PML exon 6 deletions not amplified by RQ-PCR. RT-QLAMP reproducible sensitivity is 10(-3) for bcr1 and bcr3 and 10(-)2 for bcr2 thus making this assay particularly attractive at diagnosis and leaving RQ-PCR for the molecular monitoring of minimal residual disease during the follow up. In conclusion, PML-RARA RT-QLAMP compared to RT-PCR or RQ-PCR is a valid improvement to perform rapid, simple and accurate molecular diagnosis of APL. PMID:25815362
Spinelli, Orietta; Rambaldi, Alessandro; Rigo, Francesca; Zanghì, Pamela; D'Agostini, Elena; Amicarelli, Giulia; Colotta, Francesco; Divona, Mariadomenica; Ciardi, Claudia; Coco, Francesco Lo; Minnucci, Giulia
2015-01-01
The diagnostic work-up of acute promyelocytic leukemia (APL) includes the cytogenetic demonstration of the t(15;17) translocation and/or the PML-RARA chimeric transcript by RQ-PCR or RT-PCR. This latter assays provide suitable results in 3-6 hours. We describe here two new, rapid and specific assays that detect PML-RARA transcripts, based on the RT-QLAMP (Reverse Transcription-Quenching Loop-mediated Isothermal Amplification) technology in which RNA retrotranscription and cDNA amplification are carried out in a single tube with one enzyme at one temperature, in fluorescence and real time format. A single tube triplex assay detects bcr1 and bcr3 PML-RARA transcripts along with GUS housekeeping gene. A single tube duplex assay detects bcr2 and GUSB. In 73 APL cases, these assays detected in 16 minutes bcr1, bcr2 and bcr3 transcripts. All 81 non-APL samples were negative by RT-QLAMP for chimeric transcripts whereas GUSB was detectable. In 11 APL patients in which RT-PCR yielded equivocal breakpoint type results, RT-QLAMP assays unequivocally and accurately defined the breakpoint type (as confirmed by sequencing). Furthermore, RT-QLAMP could amplify two bcr2 transcripts with particularly extended PML exon 6 deletions not amplified by RQ-PCR. RT-QLAMP reproducible sensitivity is 10−3 for bcr1 and bcr3 and 10−2 for bcr2 thus making this assay particularly attractive at diagnosis and leaving RQ-PCR for the molecular monitoring of minimal residual disease during the follow up. In conclusion, PML-RARA RT-QLAMP compared to RT-PCR or RQ-PCR is a valid improvement to perform rapid, simple and accurate molecular diagnosis of APL. PMID:25815362
PyVCI: A flexible open-source code for calculating accurate molecular infrared spectra
NASA Astrophysics Data System (ADS)
Sibaev, Marat; Crittenden, Deborah L.
2016-06-01
The PyVCI program package is a general purpose open-source code for simulating accurate molecular spectra, based upon force field expansions of the potential energy surface in normal mode coordinates. It includes harmonic normal coordinate analysis and vibrational configuration interaction (VCI) algorithms, implemented primarily in Python for accessibility but with time-consuming routines written in C. Coriolis coupling terms may be optionally included in the vibrational Hamiltonian. Non-negligible VCI matrix elements are stored in sparse matrix format to alleviate the diagonalization problem. CPU and memory requirements may be further controlled by algorithmic choices and/or numerical screening procedures, and recommended values are established by benchmarking using a test set of 44 molecules for which accurate analytical potential energy surfaces are available. Force fields in normal mode coordinates are obtained from the PyPES library of high quality analytical potential energy surfaces (to 6th order) or by numerical differentiation of analytic second derivatives generated using the GAMESS quantum chemical program package (to 4th order).
Clustering Molecular Dynamics Trajectories for Optimizing Docking Experiments
De Paris, Renata; Quevedo, Christian V.; Ruiz, Duncan D.; Norberto de Souza, Osmar; Barros, Rodrigo C.
2015-01-01
Molecular dynamics simulations of protein receptors have become an attractive tool for rational drug discovery. However, the high computational cost of employing molecular dynamics trajectories in virtual screening of large repositories threats the feasibility of this task. Computational intelligence techniques have been applied in this context, with the ultimate goal of reducing the overall computational cost so the task can become feasible. Particularly, clustering algorithms have been widely used as a means to reduce the dimensionality of molecular dynamics trajectories. In this paper, we develop a novel methodology for clustering entire trajectories using structural features from the substrate-binding cavity of the receptor in order to optimize docking experiments on a cloud-based environment. The resulting partition was selected based on three clustering validity criteria, and it was further validated by analyzing the interactions between 20 ligands and a fully flexible receptor (FFR) model containing a 20 ns molecular dynamics simulation trajectory. Our proposed methodology shows that taking into account features of the substrate-binding cavity as input for the k-means algorithm is a promising technique for accurately selecting ensembles of representative structures tailored to a specific ligand. PMID:25873944
Clustering molecular dynamics trajectories for optimizing docking experiments.
De Paris, Renata; Quevedo, Christian V; Ruiz, Duncan D; Norberto de Souza, Osmar; Barros, Rodrigo C
2015-01-01
Molecular dynamics simulations of protein receptors have become an attractive tool for rational drug discovery. However, the high computational cost of employing molecular dynamics trajectories in virtual screening of large repositories threats the feasibility of this task. Computational intelligence techniques have been applied in this context, with the ultimate goal of reducing the overall computational cost so the task can become feasible. Particularly, clustering algorithms have been widely used as a means to reduce the dimensionality of molecular dynamics trajectories. In this paper, we develop a novel methodology for clustering entire trajectories using structural features from the substrate-binding cavity of the receptor in order to optimize docking experiments on a cloud-based environment. The resulting partition was selected based on three clustering validity criteria, and it was further validated by analyzing the interactions between 20 ligands and a fully flexible receptor (FFR) model containing a 20 ns molecular dynamics simulation trajectory. Our proposed methodology shows that taking into account features of the substrate-binding cavity as input for the k-means algorithm is a promising technique for accurately selecting ensembles of representative structures tailored to a specific ligand.
Clustering molecular dynamics trajectories for optimizing docking experiments.
De Paris, Renata; Quevedo, Christian V; Ruiz, Duncan D; Norberto de Souza, Osmar; Barros, Rodrigo C
2015-01-01
Molecular dynamics simulations of protein receptors have become an attractive tool for rational drug discovery. However, the high computational cost of employing molecular dynamics trajectories in virtual screening of large repositories threats the feasibility of this task. Computational intelligence techniques have been applied in this context, with the ultimate goal of reducing the overall computational cost so the task can become feasible. Particularly, clustering algorithms have been widely used as a means to reduce the dimensionality of molecular dynamics trajectories. In this paper, we develop a novel methodology for clustering entire trajectories using structural features from the substrate-binding cavity of the receptor in order to optimize docking experiments on a cloud-based environment. The resulting partition was selected based on three clustering validity criteria, and it was further validated by analyzing the interactions between 20 ligands and a fully flexible receptor (FFR) model containing a 20 ns molecular dynamics simulation trajectory. Our proposed methodology shows that taking into account features of the substrate-binding cavity as input for the k-means algorithm is a promising technique for accurately selecting ensembles of representative structures tailored to a specific ligand. PMID:25873944
An accurate dynamical electron diffraction algorithm for reflection high-energy electron diffraction
NASA Astrophysics Data System (ADS)
Huang, J.; Cai, C. Y.; Lv, C. L.; Zhou, G. W.; Wang, Y. G.
2015-12-01
The conventional multislice method (CMS) method, one of the most popular dynamical electron diffraction calculation procedures in transmission electron microscopy, was introduced to calculate reflection high-energy electron diffraction (RHEED) as it is well adapted to deal with the deviations from the periodicity in the direction parallel to the surface. However, in the present work, we show that the CMS method is no longer sufficiently accurate for simulating RHEED with the accelerating voltage 3-100 kV because of the high-energy approximation. An accurate multislice (AMS) method can be an alternative for more accurate RHEED calculations with reasonable computing time. A detailed comparison of the numerical calculation of the AMS method and the CMS method is carried out with respect to different accelerating voltages, surface structure models, Debye-Waller factors and glancing angles.
Molecular dynamics simulations of a lithium/sodium carbonate mixture.
Ottochian, Alistar; Ricca, Chiara; Labat, Frederic; Adamo, Carlo
2016-03-01
The diffusion and ionic conductivity of Li x Na1-x CO3 salt mixtures were studied by means of Molecular Dynamics (MD) simulations, using the Janssen and Tissen model (Janssen and Tissen, Mol Simul 5:83-98; 1990). These salts have received particular attention due to their central role in fuel cells technology, and reliable numerical methods that could perform as important interpretative tool of experimental data are thus required but still lacking. The chosen computational model nicely reproduces the main structural behaviour of the pure Li2CO3, Na2CO3 and K2CO3 carbonates, but also of their Li/K and Li/Na mixtures. However, it fails to accurately describe dynamic properties such as activation energies of diffusion and conduction processes, outlining the need to develop more accurate models for the simulation of molten salt carbonates. PMID:26897519
NASA Astrophysics Data System (ADS)
Madhusudhan, Nikku; Freedman, R.; Tennyson, J.
2013-06-01
Recent advancements in exoplanet observations are placing unprecedented constraints on the physical and chemical properties of exoplanetary atmospheres. Statistically significant constraints have been placed on the abundances of atomic and molecular species, elemental abundance ratios, temperature profiles, energy circulation, presence of hazes/clouds, and non-equilibrium chemistry, in several exoplanetary atmospheres, including gas giants, ice giants, as well as super-Earths, over a wide temperature range. The chemical constraints have also motivated new paradigms for classifying exoplanets and new efforts to constraint their formation conditions. Central to all interpretations of exoplanet spectra, however, is the accuracy of fundamental inputs in the models, primarily, the atomic and molecular opacities, which are derived from laboratory experiments and/or ab initio numerical calculations. In this talk, we will review the state-of-the-art in atomic and molecular line-lists as applied to studies of exoplanetary atmospheres. We will discuss examples where advances in laboratory astrophysics, experimental and computational, have addressed important problems in the area of exoplanetary atmospheres, as well as outstanding questions requiring new experiments and/or theoretical calculations. For example, recent studies are suggesting that high-temperature line-lists of hydrocarbons (CH4, C2H2, HCN, etc.), and several metal hydrides, in addition to refined line-lists of several well-studied molecules, are important to accurately interpret exoplanetary spectra. We will highlight several fundamental questions in the area that require new efforts in laboratory astrophysics. Besides their importance in interpreting observations with current instruments, the refined parameters are also critical in the assessment of future facilities for exoplanet characterization, such as JWST, GMT, etc.
Molecular scale dynamics of large ring polymers.
Gooßen, S; Brás, A R; Krutyeva, M; Sharp, M; Falus, P; Feoktystov, A; Gasser, U; Pyckhout-Hintzen, W; Wischnewski, A; Richter, D
2014-10-17
We present neutron scattering data on the structure and dynamics of melts from polyethylene oxide rings with molecular weights up to ten times the entanglement mass of the linear counterpart. The data reveal a very compact conformation displaying a structure approaching a mass fractal, as hypothesized by recent simulation work. The dynamics is characterized by a fast Rouse relaxation of subunits (loops) and a slower dynamics displaying a lattice animal-like loop displacement. The loop size is an intrinsic property of the ring architecture and is independent of molecular weight. This is the first experimental observation of the space-time evolution of segmental motion in ring polymers illustrating the dynamic consequences of their topology that is unique among all polymeric systems of any other known architecture. PMID:25361284
Dynamic signature of molecular association in methanol.
Bertrand, C E; Self, J L; Copley, J R D; Faraone, A
2016-07-01
Quasielastic neutron scattering measurements and molecular dynamics simulations were combined to investigate the collective dynamics of deuterated methanol, CD3OD. In the experimentally determined dynamic structure factor, a slow, non-Fickian mode was observed in addition to the standard density-fluctuation heat mode. The simulation results indicate that the slow dynamical process originates from the hydrogen bonding of methanol molecules. The qualitative behavior of this mode is similar to the previously observed α-relaxation in supercooled water [M. C. Bellissent-Funel et al., Phys. Rev. Lett. 85, 3644 (2000)] which also originates from the formation and dissolution of hydrogen-bonded associates (supramolecular clusters). In methanol, however, this mode is distinguishable well above the freezing transition. This finding indicates that an emergent slow mode is not unique to supercooled water, but may instead be a general feature of hydrogen-bonding liquids and associating molecular liquids. PMID:27394112
Molecular scale dynamics of large ring polymers.
Gooßen, S; Brás, A R; Krutyeva, M; Sharp, M; Falus, P; Feoktystov, A; Gasser, U; Pyckhout-Hintzen, W; Wischnewski, A; Richter, D
2014-10-17
We present neutron scattering data on the structure and dynamics of melts from polyethylene oxide rings with molecular weights up to ten times the entanglement mass of the linear counterpart. The data reveal a very compact conformation displaying a structure approaching a mass fractal, as hypothesized by recent simulation work. The dynamics is characterized by a fast Rouse relaxation of subunits (loops) and a slower dynamics displaying a lattice animal-like loop displacement. The loop size is an intrinsic property of the ring architecture and is independent of molecular weight. This is the first experimental observation of the space-time evolution of segmental motion in ring polymers illustrating the dynamic consequences of their topology that is unique among all polymeric systems of any other known architecture.
Dynamic signature of molecular association in methanol
NASA Astrophysics Data System (ADS)
Bertrand, C. E.; Self, J. L.; Copley, J. R. D.; Faraone, A.
2016-07-01
Quasielastic neutron scattering measurements and molecular dynamics simulations were combined to investigate the collective dynamics of deuterated methanol, CD3OD. In the experimentally determined dynamic structure factor, a slow, non-Fickian mode was observed in addition to the standard density-fluctuation heat mode. The simulation results indicate that the slow dynamical process originates from the hydrogen bonding of methanol molecules. The qualitative behavior of this mode is similar to the previously observed α-relaxation in supercooled water [M. C. Bellissent-Funel et al., Phys. Rev. Lett. 85, 3644 (2000)] which also originates from the formation and dissolution of hydrogen-bonded associates (supramolecular clusters). In methanol, however, this mode is distinguishable well above the freezing transition. This finding indicates that an emergent slow mode is not unique to supercooled water, but may instead be a general feature of hydrogen-bonding liquids and associating molecular liquids.
Semiclassical guided optimal control of molecular dynamics
Kondorskiy, A.; Mil'nikov, G.; Nakamura, H.
2005-10-15
An efficient semiclassical optimal control theory applicable to multidimensional systems is formulated for controlling wave packet dynamics on a single adiabatic potential energy surface. The approach combines advantages of different formulations of optimal control theory: quantum and classical on one hand and global and local on the other. Numerical applications to the control of HCN-CNH isomerization demonstrate that this theory can provide an efficient tool to manipulate molecular dynamics of many degrees of freedom by laser pulses.
Approximate but accurate quantum dynamics from the Mori formalism: I. Nonequilibrium dynamics.
Montoya-Castillo, Andrés; Reichman, David R
2016-05-14
We present a formalism that explicitly unifies the commonly used Nakajima-Zwanzig approach for reduced density matrix dynamics with the more versatile Mori theory in the context of nonequilibrium dynamics. Employing a Dyson-type expansion to circumvent the difficulty of projected dynamics, we obtain a self-consistent equation for the memory kernel which requires only knowledge of normally evolved auxiliary kernels. To illustrate the properties of the current approach, we focus on the spin-boson model and limit our attention to the use of a simple and inexpensive quasi-classical dynamics, given by the Ehrenfest method, for the calculation of the auxiliary kernels. For the first time, we provide a detailed analysis of the dependence of the properties of the memory kernels obtained via different projection operators, namely, the thermal (Redfield-type) and population based (NIBA-type) projection operators. We further elucidate the conditions that lead to short-lived memory kernels and the regions of parameter space to which this program is best suited. Via a thorough analysis of the different closures available for the auxiliary kernels and the convergence properties of the self-consistently extracted memory kernel, we identify the mechanisms whereby the current approach leads to a significant improvement over the direct usage of standard semi- and quasi-classical dynamics. PMID:27179468
Approximate but accurate quantum dynamics from the Mori formalism: I. Nonequilibrium dynamics
NASA Astrophysics Data System (ADS)
Montoya-Castillo, Andrés; Reichman, David R.
2016-05-01
We present a formalism that explicitly unifies the commonly used Nakajima-Zwanzig approach for reduced density matrix dynamics with the more versatile Mori theory in the context of nonequilibrium dynamics. Employing a Dyson-type expansion to circumvent the difficulty of projected dynamics, we obtain a self-consistent equation for the memory kernel which requires only knowledge of normally evolved auxiliary kernels. To illustrate the properties of the current approach, we focus on the spin-boson model and limit our attention to the use of a simple and inexpensive quasi-classical dynamics, given by the Ehrenfest method, for the calculation of the auxiliary kernels. For the first time, we provide a detailed analysis of the dependence of the properties of the memory kernels obtained via different projection operators, namely, the thermal (Redfield-type) and population based (NIBA-type) projection operators. We further elucidate the conditions that lead to short-lived memory kernels and the regions of parameter space to which this program is best suited. Via a thorough analysis of the different closures available for the auxiliary kernels and the convergence properties of the self-consistently extracted memory kernel, we identify the mechanisms whereby the current approach leads to a significant improvement over the direct usage of standard semi- and quasi-classical dynamics.
Thompson, Andrew R; Binder, Benjamin P; McCaffrey, Jesse E; Svensson, Bengt; Thomas, David D
2015-01-01
While EPR allows for the characterization of protein structure and function due to its exquisite sensitivity to spin label dynamics, orientation, and distance, these measurements are often limited in sensitivity due to the use of labels that are attached via flexible monofunctional bonds, incurring additional disorder and nanosecond dynamics. In this chapter, we present methods for using a bifunctional spin label (BSL) to measure muscle protein structure and dynamics. We demonstrate that bifunctional attachment eliminates nanosecond internal rotation of the spin label, thereby allowing the accurate measurement of protein backbone rotational dynamics, including microsecond-to-millisecond motions by saturation transfer EPR. BSL also allows for accurate determination of helix orientation and disorder in mechanically and magnetically aligned systems, due to the label's stereospecific attachment. Similarly, labeling with a pair of BSL greatly enhances the resolution and accuracy of distance measurements measured by double electron-electron resonance (DEER). Finally, when BSL is applied to a protein with high helical content in an assembly with high orientational order (e.g., muscle fiber or membrane), two-probe DEER experiments can be combined with single-probe EPR experiments on an oriented sample in a process we call BEER, which has the potential for ab initio high-resolution structure determination. PMID:26477249
Shapiro like steps reveals molecular nanomagnets’ spin dynamics
Abdollahipour, Babak; Abouie, Jahanfar Ebrahimi, Navid
2015-09-15
We present an accurate way to detect spin dynamics of a nutating molecular nanomagnet by inserting it in a tunnel Josephson junction and studying the current voltage (I-V) characteristic. The spin nutation of the molecular nanomagnet is generated by applying two circularly polarized magnetic fields. We demonstrate that modulation of the Josephson current by the nutation of the molecular nanomagnet’s spin appears as a stepwise structure like Shapiro steps in the I-V characteristic of the junction. Width and heights of these Shapiro-like steps are determined by two parameters of the spin nutation, frequency and amplitude of the nutation, which are simply tuned by the applied magnetic fields.
Molecular Dynamics Simulation of a Microvillus in a Cross Flow
NASA Astrophysics Data System (ADS)
Chen, X. Y.; Liu, Y.; So, R. M. C.; Yang, J. M.
One of the functions of microvilli in the microvessel endothelial glycocalyx is molecular filtering. The microvillus behaves as a mechanosensory system which may sense the fluid shear and drag forces. The permeability of small particles in microvessel is crucial for drug design and drug delivery. Therefore a better understanding of flow field around microvillus is important to simulate accurately the particle penetration in microvessel. Since the dimension of the microvilli is about ~10 nm, the conventional Navier-Stokes equation may not be good enough to simulate the fluid flow in such microscale and nanoscale structures. Molecular dynamics (MD) simulation is a powerful method to simulate the fluid flow at the molecular level. As a first attempt, the microvillus is reduced as a two-dimensional cylinder which is in a cross flow. The detailed drag and lift together with flow field are obtained and compared with available data.
Hansen, D Flemming; Westler, William M; Kunze, Micha B A; Markley, John L; Weinhold, Frank; Led, Jens J
2012-03-14
A natural bond orbital (NBO) analysis of unpaired electron spin density in metalloproteins is presented, which allows a fast and robust calculation of paramagnetic NMR parameters. Approximately 90% of the unpaired electron spin density occupies metal-ligand NBOs, allowing the majority of the density to be modeled by only a few NBOs that reflect the chemical bonding environment. We show that the paramagnetic relaxation rate of protons can be calculated accurately using only the metal-ligand NBOs and that these rates are in good agreement with corresponding rates measured experimentally. This holds, in particular, for protons of ligand residues where the point-dipole approximation breaks down. To describe the paramagnetic relaxation of heavy nuclei, also the electron spin density in the local orbitals must be taken into account. Geometric distance restraints for (15)N can be derived from the paramagnetic relaxation enhancement and the Fermi contact shift when local NBOs are included in the analysis. Thus, the NBO approach allows us to include experimental paramagnetic NMR parameters of (15)N nuclei as restraints in a structure optimization protocol. We performed a molecular dynamics simulation and structure determination of oxidized rubredoxin using the experimentally obtained paramagnetic NMR parameters of (15)N. The corresponding structures obtained are in good agreement with the crystal structure of rubredoxin. Thus, the NBO approach allows an accurate description of the geometric structure and the dynamics of metalloproteins, when NMR parameters are available of nuclei in the immediate vicinity of the metal-site.
2012-01-01
A natural bond orbital (NBO) analysis of unpaired electron spin density in metalloproteins is presented, which allows a fast and robust calculation of paramagnetic NMR parameters. Approximately 90% of the unpaired electron spin density occupies metal–ligand NBOs, allowing the majority of the density to be modeled by only a few NBOs that reflect the chemical bonding environment. We show that the paramagnetic relaxation rate of protons can be calculated accurately using only the metal–ligand NBOs and that these rates are in good agreement with corresponding rates measured experimentally. This holds, in particular, for protons of ligand residues where the point-dipole approximation breaks down. To describe the paramagnetic relaxation of heavy nuclei, also the electron spin density in the local orbitals must be taken into account. Geometric distance restraints for 15N can be derived from the paramagnetic relaxation enhancement and the Fermi contact shift when local NBOs are included in the analysis. Thus, the NBO approach allows us to include experimental paramagnetic NMR parameters of 15N nuclei as restraints in a structure optimization protocol. We performed a molecular dynamics simulation and structure determination of oxidized rubredoxin using the experimentally obtained paramagnetic NMR parameters of 15N. The corresponding structures obtained are in good agreement with the crystal structure of rubredoxin. Thus, the NBO approach allows an accurate description of the geometric structure and the dynamics of metalloproteins, when NMR parameters are available of nuclei in the immediate vicinity of the metal-site. PMID:22329704
Molecular Exchange Dynamics in Block Copolymer Micelles
NASA Astrophysics Data System (ADS)
Bates, Frank; Lu, Jie; Choi, Soohyung; Lodge, Timothy
2012-02-01
Poly(styrene-b-ethylene propylene) (PS-PEP) diblock copolymers were mixed with squalane (C30H62) at 1% by weight resulting in the formation of spherical micelles. The structure and dynamics of molecular exchange were characterized by synchrotron small-angle x-ray scattering (SAXS) and time resolved small-angle neutron scattering (TR-SANS), respectively, between 100 C and 160 C. TR-SANS measurements were performed with solutions initially containing deuterium labeled micelle cores and normal cores dispersed in a contrast matched squalane. Monitoring the reduction in scattering intensity as a function of time at various temperatures revealed molecular exchange dynamics highly sensitive to the core molecular weight and molecular weight distribution. Time-temperature superposition of data acquired at different temperatures produced a single master curve for all the mixtures. Experiments conducted with isotopically labeled micelle cores, each formed from two different but relatively mondisperse PS blocks, confirmed a simple dynamical model based on first order kinetics and core Rouse single chain relaxation. These findings demonstrate a dramatic transition to nonergodicity with increasing micelle core molecular weight and confirm the origins of the logarithmic exchange kinetics in such systems.
Reaction dynamics in polyatomic molecular systems
Miller, W.H.
1993-12-01
The goal of this program is the development of theoretical methods and models for describing the dynamics of chemical reactions, with specific interest for application to polyatomic molecular systems of special interest and relevance. There is interest in developing the most rigorous possible theoretical approaches and also in more approximate treatments that are more readily applicable to complex systems.
Accurate calculation of binding energies for molecular clusters - Assessment of different models
NASA Astrophysics Data System (ADS)
Friedrich, Joachim; Fiedler, Benjamin
2016-06-01
In this work we test different strategies to compute high-level benchmark energies for medium-sized molecular clusters. We use the incremental scheme to obtain CCSD(T)/CBS energies for our test set and carefully validate the accuracy for binding energies by statistical measures. The local errors of the incremental scheme are <1 kJ/mol. Since they are smaller than the basis set errors, we obtain higher total accuracy due to the applicability of larger basis sets. The final CCSD(T)/CBS benchmark values are ΔE = - 278.01 kJ/mol for (H2O)10, ΔE = - 221.64 kJ/mol for (HF)10, ΔE = - 45.63 kJ/mol for (CH4)10, ΔE = - 19.52 kJ/mol for (H2)20 and ΔE = - 7.38 kJ/mol for (H2)10 . Furthermore we test state-of-the-art wave-function-based and DFT methods. Our benchmark data will be very useful for critical validations of new methods. We find focal-point-methods for estimating CCSD(T)/CBS energies to be highly accurate and efficient. For foQ-i3CCSD(T)-MP2/TZ we get a mean error of 0.34 kJ/mol and a standard deviation of 0.39 kJ/mol.
An efficient and accurate molecular alignment and docking technique using ab initio quality scoring
Füsti-Molnár, László; Merz, Kenneth M.
2008-01-01
An accurate and efficient molecular alignment technique is presented based on first principle electronic structure calculations. This new scheme maximizes quantum similarity matrices in the relative orientation of the molecules and uses Fourier transform techniques for two purposes. First, building up the numerical representation of true ab initio electronic densities and their Coulomb potentials is accelerated by the previously described Fourier transform Coulomb method. Second, the Fourier convolution technique is applied for accelerating optimizations in the translational coordinates. In order to avoid any interpolation error, the necessary analytical formulas are derived for the transformation of the ab initio wavefunctions in rotational coordinates. The results of our first implementation for a small test set are analyzed in detail and compared with published results of the literature. A new way of refinement of existing shape based alignments is also proposed by using Fourier convolutions of ab initio or other approximate electron densities. This new alignment technique is generally applicable for overlap, Coulomb, kinetic energy, etc., quantum similarity measures and can be extended to a genuine docking solution with ab initio scoring. PMID:18624561
NASA Astrophysics Data System (ADS)
Feller, David; Peterson, Kirk A.; Dixon, David A.
2008-11-01
High level electronic structure predictions of thermochemical properties and molecular structure are capable of accuracy rivaling the very best experimental measurements as a result of rapid advances in hardware, software, and methodology. Despite the progress, real world limitations require practical approaches designed for handling general chemical systems that rely on composite strategies in which a single, intractable calculation is replaced by a series of smaller calculations. As typically implemented, these approaches produce a final, or "best," estimate that is constructed from one major component, fine-tuned by multiple corrections that are assumed to be additive. Though individually much smaller than the original, unmanageable computational problem, these corrections are nonetheless extremely costly. This study presents a survey of the widely varying magnitude of the most important components contributing to the atomization energies and structures of 106 small molecules. It combines large Gaussian basis sets and coupled cluster theory up to quadruple excitations for all systems. In selected cases, the effects of quintuple excitations and/or full configuration interaction were also considered. The availability of reliable experimental data for most of the molecules permits an expanded statistical analysis of the accuracy of the approach. In cases where reliable experimental information is currently unavailable, the present results are expected to provide some of the most accurate benchmark values available.
Multiscale coupling of molecular dynamics and peridynamics
NASA Astrophysics Data System (ADS)
Tong, Qi; Li, Shaofan
2016-10-01
We propose a multiscale computational model to couple molecular dynamics and peridynamics. The multiscale coupling model is based on a previously developed multiscale micromorphic molecular dynamics (MMMD) theory, which has three dynamics equations at three different scales, namely, microscale, mesoscale, and macroscale. In the proposed multiscale coupling approach, we divide the simulation domain into atomistic region and macroscale region. Molecular dynamics is used to simulate atom motions in atomistic region, and peridynamics is used to simulate macroscale material point motions in macroscale region, and both methods are nonlocal particle methods. A transition zone is introduced as a messenger to pass the information between the two regions or scales. We employ the "supercell" developed in the MMMD theory as the transition element, which is named as the adaptive multiscale element due to its ability of passing information from different scales, because the adaptive multiscale element can realize both top-down and bottom-up communications. We introduce the Cauchy-Born rule based stress evaluation into state-based peridynamics formulation to formulate atomistic-enriched constitutive relations. To mitigate the issue of wave reflection on the interface, a filter is constructed by switching on and off the MMMD dynamic equations at different scales. Benchmark tests of one-dimensional (1-D) and two-dimensional (2-D) wave propagations from atomistic region to macro region are presented. The mechanical wave can transit through the interface smoothly without spurious wave deflections, and the filtering process is proven to be efficient.
MDMovie: a molecular dynamics viewing tool.
Greenberg, J P
1996-10-01
The graphics program MDMovie (Molecular Dynamics Movie), written in C using IRIS GL graphics library calls, is designed to facilitate the visualization and interpretation of empirical force field data. MDMovie was created and initially adapted in accord with the needs of physical chemists and thereafter became an expandable analysis tool. Capabilities include the display of chemical structure, animation of molecular dynamics and Monte Carlo trajectories, and the visual representation of various vector and scalar dynamical properties. In addition to being a research tool, MDMovie has features for creating presentation videos and hardcopy output. A library is also available for linking to Fortran simulation codes running on a remote machine and connecting to MDMovie via a socket connection. MDMovie continues to be an ongoing research project and new features are actively being added in collaboration with various research groups. Future plans include porting to OpenGL and the design of an XII-based user interface.
Structural and dynamical properties of hot dense matter by a Thomas-Fermi-Dirac molecular dynamics
NASA Astrophysics Data System (ADS)
Lambert, F.; Clérouin, J.; Mazevet, S.
2006-09-01
We use a model combining, in a consistent way, orbital-free density functional theory (OF-DFT) and molecular dynamics (MD), to compute the thermodynamical, structural and dynamical properties of Fe and Au plasmas at conditions relevant to astrophysics and inertial confinement fusion (ICF). The newly developed parallel numerical scheme presented here allows to propagate hundreds of particles and to obtain accurate transport properties. This allows us to investigate the validity of the commonly used one-component plasma (OCP) model in predicting the pair correlation, the diffusion and viscosity coefficients for these two high-temperature high-density plasmas.
Calcium Binding to Calmodulin by Molecular Dynamics with Effective Polarization.
Kohagen, Miriam; Lepšík, Martin; Jungwirth, Pavel
2014-11-20
Calcium represents a key biological signaling ion with the EF-hand loops being its most prevalent binding motif in proteins. We show using molecular dynamics simulations with umbrella sampling that including electronic polarization effects via ionic charge rescaling dramatically improves agreements with experiment in terms of the strength of calcium binding and structures of the calmodulin binding sites. The present study thus opens way to accurate calculations of interactions of calcium and other computationally difficult high-charge-density ions in biological contexts.
Parallel-in-time molecular-dynamics simulations.
Baffico, L; Bernard, S; Maday, Y; Turinici, G; Zérah, G
2002-11-01
While there have been many progress in the field of multiscale simulations in the space domain, in particular, due to efficient parallelization techniques, much less is known in the way to perform similar approaches in the time domain. In this paper we show on two examples that, provided we can describe in a rough but still accurate way the system under consideration, it is indeed possible to parallelize molecular dynamics simulations in time by using the recently introduced pararealalgorithm. The technique is most useful for ab initio simulations. PMID:12513644
Parallel-in-time molecular-dynamics simulations
NASA Astrophysics Data System (ADS)
Baffico, L.; Bernard, S.; Maday, Y.; Turinici, G.; Zérah, G.
2002-11-01
While there have been many progress in the field of multiscale simulations in the space domain, in particular, due to efficient parallelization techniques, much less is known in the way to perform similar approaches in the time domain. In this paper we show on two examples that, provided we can describe in a rough but still accurate way the system under consideration, it is indeed possible to parallelize molecular dynamics simulations in time by using the recently introduced pararealalgorithm. The technique is most useful for ab initio simulations.
An accurate scheme to solve cluster dynamics equations using a Fokker-Planck approach
NASA Astrophysics Data System (ADS)
Jourdan, T.; Stoltz, G.; Legoll, F.; Monasse, L.
2016-10-01
We present a numerical method to accurately simulate particle size distributions within the formalism of rate equation cluster dynamics. This method is based on a discretization of the associated Fokker-Planck equation. We show that particular care has to be taken to discretize the advection part of the Fokker-Planck equation, in order to avoid distortions of the distribution due to numerical diffusion. For this purpose we use the Kurganov-Noelle-Petrova scheme coupled with the monotonicity-preserving reconstruction MP5, which leads to very accurate results. The interest of the method is highlighted in the case of loop coarsening in aluminum. We show that the choice of the models to describe the energetics of loops does not significantly change the normalized loop distribution, while the choice of the models for the absorption coefficients seems to have a significant impact on it.
A multiscale red blood cell model with accurate mechanics, rheology, and dynamics.
Fedosov, Dmitry A; Caswell, Bruce; Karniadakis, George Em
2010-05-19
Red blood cells (RBCs) have highly deformable viscoelastic membranes exhibiting complex rheological response and rich hydrodynamic behavior governed by special elastic and bending properties and by the external/internal fluid and membrane viscosities. We present a multiscale RBC model that is able to predict RBC mechanics, rheology, and dynamics in agreement with experiments. Based on an analytic theory, the modeled membrane properties can be uniquely related to the experimentally established RBC macroscopic properties without any adjustment of parameters. The RBC linear and nonlinear elastic deformations match those obtained in optical-tweezers experiments. The rheological properties of the membrane are compared with those obtained in optical magnetic twisting cytometry, membrane thermal fluctuations, and creep followed by cell recovery. The dynamics of RBCs in shear and Poiseuille flows is tested against experiments and theoretical predictions, and the applicability of the latter is discussed. Our findings clearly indicate that a purely elastic model for the membrane cannot accurately represent the RBC's rheological properties and its dynamics, and therefore accurate modeling of a viscoelastic membrane is necessary.
A Multiscale Red Blood Cell Model with Accurate Mechanics, Rheology, and Dynamics
Fedosov, Dmitry A.; Caswell, Bruce; Karniadakis, George Em
2010-01-01
Abstract Red blood cells (RBCs) have highly deformable viscoelastic membranes exhibiting complex rheological response and rich hydrodynamic behavior governed by special elastic and bending properties and by the external/internal fluid and membrane viscosities. We present a multiscale RBC model that is able to predict RBC mechanics, rheology, and dynamics in agreement with experiments. Based on an analytic theory, the modeled membrane properties can be uniquely related to the experimentally established RBC macroscopic properties without any adjustment of parameters. The RBC linear and nonlinear elastic deformations match those obtained in optical-tweezers experiments. The rheological properties of the membrane are compared with those obtained in optical magnetic twisting cytometry, membrane thermal fluctuations, and creep followed by cell recovery. The dynamics of RBCs in shear and Poiseuille flows is tested against experiments and theoretical predictions, and the applicability of the latter is discussed. Our findings clearly indicate that a purely elastic model for the membrane cannot accurately represent the RBC's rheological properties and its dynamics, and therefore accurate modeling of a viscoelastic membrane is necessary. PMID:20483330
Polar solvation dynamics of lysozyme from molecular dynamics studies
NASA Astrophysics Data System (ADS)
Sinha, Sudipta Kumar; Bandyopadhyay, Sanjoy
2012-05-01
The solvation dynamics of a protein are believed to be sensitive to its secondary structures. We have explored such sensitivity in this article by performing room temperature molecular dynamics simulation of an aqueous solution of lysozyme. Nonuniform long-time relaxation patterns of the solvation time correlation function for different segments of the protein have been observed. It is found that relatively slower long-time solvation components of the α-helices and β-sheets of the protein are correlated with lower exposure of their polar probe residues to bulk solvent and hence stronger interactions with the dynamically restricted surface water molecules. These findings can be verified by appropriate experimental studies.
Nonadiabatic molecular dynamics simulations: synergies between theory and experiments.
Tavernelli, Ivano
2015-03-17
Recent developments in nonadiabatic dynamics enabled ab inito simulations of complex ultrafast processes in the condensed phase. These advances have opened new avenues in the study of many photophysical and photochemical reactions triggered by the absorption of electromagnetic radiation. In particular, theoretical investigations can be combined with the most sophisticated femtosecond experimental techniques to guide the interpretation of measured time-resolved observables. At the same time, the availability of experimental data at high (spatial and time) resolution offers a unique opportunity for the benchmarking and the improvement of those theoretical models used to describe complex molecular systems in their natural environment. The established synergy between theory and experiments can produce a better understanding of new ultrafast physical and chemical processes at atomistic scale resolution. Furthermore, reliable ab inito molecular dynamics simulations can already be successfully employed as predictive tools to guide new experiments as well as the design of novel and better performing materials. In this paper, I will give a concise account on the state of the art of molecular dynamics simulations of complex molecular systems in their excited states. The principal aim of this approach is the description of a given system of interest under the most realistic ambient conditions including all environmental effects that influence experiments, for instance, the interaction with the solvent and with external time-dependent electric fields, temperature, and pressure. To this end, time-dependent density functional theory (TDDFT) is among the most efficient and accurate methods for the representation of the electronic dynamics, while trajectory surface hopping gives a valuable representation of the nuclear quantum dynamics in the excited states (including nonadiabatic effects). Concerning the environment and its effects on the dynamics, the quantum mechanics/molecular
Nonadiabatic molecular dynamics simulations: synergies between theory and experiments.
Tavernelli, Ivano
2015-03-17
Recent developments in nonadiabatic dynamics enabled ab inito simulations of complex ultrafast processes in the condensed phase. These advances have opened new avenues in the study of many photophysical and photochemical reactions triggered by the absorption of electromagnetic radiation. In particular, theoretical investigations can be combined with the most sophisticated femtosecond experimental techniques to guide the interpretation of measured time-resolved observables. At the same time, the availability of experimental data at high (spatial and time) resolution offers a unique opportunity for the benchmarking and the improvement of those theoretical models used to describe complex molecular systems in their natural environment. The established synergy between theory and experiments can produce a better understanding of new ultrafast physical and chemical processes at atomistic scale resolution. Furthermore, reliable ab inito molecular dynamics simulations can already be successfully employed as predictive tools to guide new experiments as well as the design of novel and better performing materials. In this paper, I will give a concise account on the state of the art of molecular dynamics simulations of complex molecular systems in their excited states. The principal aim of this approach is the description of a given system of interest under the most realistic ambient conditions including all environmental effects that influence experiments, for instance, the interaction with the solvent and with external time-dependent electric fields, temperature, and pressure. To this end, time-dependent density functional theory (TDDFT) is among the most efficient and accurate methods for the representation of the electronic dynamics, while trajectory surface hopping gives a valuable representation of the nuclear quantum dynamics in the excited states (including nonadiabatic effects). Concerning the environment and its effects on the dynamics, the quantum mechanics/molecular
Molecular dynamics analysis on impact behavior of carbon nanotubes
NASA Astrophysics Data System (ADS)
Seifoori, Sajjad
2015-01-01
Dynamic analysis of impact of a nanoparticle on carbon nanotubes is investigated based on two degree of freedom model. The accuracy and stability of the present methods are verified by molecular dynamics (MD) simulations. The effect of different types of boundary condition on the maximum dynamic deflections is studied for zigzag and armchair SWCNTs with various aspect ratios (length/diameter). Besides, the influences of velocity of impactor on the dynamic deflections are studied. It is shown that the dynamic behavior on the armchair and zigzag single-walled carbon nanotubes are almost similar. Finally, by making use of the above MD simulation and theoretical results some insight has been obtained about the dynamic characteristics of the impact problems of nanobeam structures. Nonlocal Timoshenko beam models TBT2 should be employed for an accurate prediction of the dynamic deflection rather than nonlocal Euler-Bernoulli beam models EBT2 which ignores the effects of transverse shear deformation and rotary inertia that is especially significant for short beams. The results from nonlocal EBT2 and TBT2 models demonstrated good agreement with MD simulation. The EBT2 and TBT2 models also account for the relative motion between the nanoparticle and the nanobeam that is due to local indentation as can be seen in MD simulation.
Puzzarini, Cristina; Biczysko, Malgorzata; Barone, Vincenzo; Peña, Isabel; Cabezas, Carlos; Alonso, José L.
2015-01-01
The computational composite scheme purposely set up for accurately describing the electronic structure and spectroscopic properties of small biomolecules has been applied to the first study of the rotational spectrum of 2-thiouracil. The experimental investigation was made possible thanks to the combination of the laser ablation technique with Fourier Transform Microwave spectrometers. The joint experimental – computational study allowed us to determine accurate molecular structure and spectroscopic properties for the title molecule, but more important, it demonstrates a reliable approach for the accurate investigation of isolated small biomolecules. PMID:24002739
Deng, Yan; Zhou, Bin; Xing, Chao; Zhang, Rong
2014-10-17
A novel multifrequency excitation (MFE) method is proposed to realize rapid and accurate dynamic testing of micromachined gyroscope chips. Compared with the traditional sweep-frequency excitation (SFE) method, the computational time for testing one chip under four modes at a 1-Hz frequency resolution and 600-Hz bandwidth was dramatically reduced from 10 min to 6 s. A multifrequency signal with an equal amplitude and initial linear-phase-difference distribution was generated to ensure test repeatability and accuracy. The current test system based on LabVIEW using the SFE method was modified to use the MFE method without any hardware changes. The experimental results verified that the MFE method can be an ideal solution for large-scale dynamic testing of gyroscope chips and gyroscopes.
Deng, Yan; Zhou, Bin; Xing, Chao; Zhang, Rong
2014-01-01
A novel multifrequency excitation (MFE) method is proposed to realize rapid and accurate dynamic testing of micromachined gyroscope chips. Compared with the traditional sweep-frequency excitation (SFE) method, the computational time for testing one chip under four modes at a 1-Hz frequency resolution and 600-Hz bandwidth was dramatically reduced from 10 min to 6 s. A multifrequency signal with an equal amplitude and initial linear-phase-difference distribution was generated to ensure test repeatability and accuracy. The current test system based on LabVIEW using the SFE method was modified to use the MFE method without any hardware changes. The experimental results verified that the MFE method can be an ideal solution for large-scale dynamic testing of gyroscope chips and gyroscopes. PMID:25330052
Dynamic strength of molecular adhesion bonds.
Evans, E; Ritchie, K
1997-01-01
In biology, molecular linkages at, within, and beneath cell interfaces arise mainly from weak noncovalent interactions. These bonds will fail under any level of pulling force if held for sufficient time. Thus, when tested with ultrasensitive force probes, we expect cohesive material strength and strength of adhesion at interfaces to be time- and loading rate-dependent properties. To examine what can be learned from measurements of bond strength, we have extended Kramers' theory for reaction kinetics in liquids to bond dissociation under force and tested the predictions by smart Monte Carlo (Brownian dynamics) simulations of bond rupture. By definition, bond strength is the force that produces the most frequent failure in repeated tests of breakage, i.e., the peak in the distribution of rupture forces. As verified by the simulations, theory shows that bond strength progresses through three dynamic regimes of loading rate. First, bond strength emerges at a critical rate of loading (> or = 0) at which spontaneous dissociation is just frequent enough to keep the distribution peak at zero force. In the slow-loading regime immediately above the critical rate, strength grows as a weak power of loading rate and reflects initial coupling of force to the bonding potential. At higher rates, there is crossover to a fast regime in which strength continues to increase as the logarithm of the loading rate over many decades independent of the type of attraction. Finally, at ultrafast loading rates approaching the domain of molecular dynamics simulations, the bonding potential is quickly overwhelmed by the rapidly increasing force, so that only naked frictional drag on the structure remains to retard separation. Hence, to expose the energy landscape that governs bond strength, molecular adhesion forces must be examined over an enormous span of time scales. However, a significant gap exists between the time domain of force measurements in the laboratory and the extremely fast scale
Dynamical quenching of tunneling in molecular magnets
NASA Astrophysics Data System (ADS)
José Santander, María; Nunez, Alvaro S.; Roldán-Molina, A.; Troncoso, Roberto E.
2015-12-01
It is shown that a single molecular magnet placed in a rapidly oscillating magnetic field displays the phenomenon of quenching of tunneling processes. The results open a way to manipulate the quantum states of molecular magnets by means of radiation in the terahertz range. Our analysis separates the time evolution into slow and fast components thereby obtaining an effective theory for the slow dynamics. This effective theory presents quenching of the tunnel effect, in particular, stands out its difference with the so-called coherent destruction of tunneling. We support our prediction with numerical evidence based on an exact solution of Schrödinger's equation.
Exciton dynamics in perturbed vibronic molecular aggregates
Brüning, C.; Wehner, J.; Hausner, J.; Wenzel, M.; Engel, V.
2015-01-01
A site specific perturbation of a photo-excited molecular aggregate can lead to a localization of excitonic energy. We investigate this localization dynamics for laser-prepared excited states. Changing the parameters of the electric field significantly influences the exciton localization which offers the possibility for a selective control of this process. This is demonstrated for aggregates possessing a single vibrational degree of freedom per monomer unit. It is shown that the effects identified for the molecular dimer can be generalized to larger aggregates with a high density of vibronic states. PMID:26798840
Exploiting molecular dynamics in Nested Sampling simulations of small peptides
NASA Astrophysics Data System (ADS)
Burkoff, Nikolas S.; Baldock, Robert J. N.; Várnai, Csilla; Wild, David L.; Csányi, Gábor
2016-04-01
Nested Sampling (NS) is a parameter space sampling algorithm which can be used for sampling the equilibrium thermodynamics of atomistic systems. NS has previously been used to explore the potential energy surface of a coarse-grained protein model and has significantly outperformed parallel tempering when calculating heat capacity curves of Lennard-Jones clusters. The original NS algorithm uses Monte Carlo (MC) moves; however, a variant, Galilean NS, has recently been introduced which allows NS to be incorporated into a molecular dynamics framework, so NS can be used for systems which lack efficient prescribed MC moves. In this work we demonstrate the applicability of Galilean NS to atomistic systems. We present an implementation of Galilean NS using the Amber molecular dynamics package and demonstrate its viability by sampling alanine dipeptide, both in vacuo and implicit solvent. Unlike previous studies of this system, we present the heat capacity curves of alanine dipeptide, whose calculation provides a stringent test for sampling algorithms. We also compare our results with those calculated using replica exchange molecular dynamics (REMD) and find good agreement. We show the computational effort required for accurate heat capacity estimation for small peptides. We also calculate the alanine dipeptide Ramachandran free energy surface for a range of temperatures and use it to compare the results using the latest Amber force field with previous theoretical and experimental results.
Concise NMR approach for molecular dynamics characterizations in organic solids.
Aliev, Abil E; Courtier-Murias, Denis
2013-08-22
Molecular dynamics characterisations in solids can be carried out selectively using dipolar-dephasing experiments. Here we show that the introduction of a sum of Lorentzian and Gaussian functions greatly improve fittings of the "intensity versus time" data for protonated carbons in dipolar-dephasing experiments. The Lorentzian term accounts for remote intra- and intermolecular (1)H-(13)C dipole-dipole interactions, which vary from one molecule to another or for different carbons within the same molecule. Thus, by separating contributions from weak remote interactions, more accurate Gaussian decay constants, T(dd), can be extracted for directly bonded (1)H-(13)C dipole-dipole interactions. Reorientations of the (1)H-(13)C bonds lead to the increase of T(dd), and by measuring dipolar-dephasing constants, insight can be gained into dynamics in solids. We have demonstrated advantages of the method using comparative dynamics studies in the α and γ polymorphs of glycine, cyclic amino acids L-proline, DL-proline and trans-4-hydroxy-L-proline, the Ala residue in different dipeptides, as well as adamantane and hexamethylenetetramine. It was possible to distinguish subtle differences in dynamics of different carbon sites within a molecule in polymorphs and in L- and DL-forms. The presence of overall molecular motions is shown to lead to particularly large differences in dipolar-dephasing experiments. The differences in dynamics can be attributed to differences in noncovalent interactions. In the case of hexamethylenetetramine, for example, the presence of C-H···N interactions leads to nearly rigid molecules. Overall, the method allows one to gain insight into the role of noncovalent interactions in solids and their influence on the molecular dynamics.
Molecular dynamic simulation methods for anisotropic liquids.
Aoki, Keiko M; Yoneya, Makoto; Yokoyama, Hiroshi
2004-03-22
Methods of molecular dynamics simulations for anisotropic molecules are presented. The new methods, with an anisotropic factor in the cell dynamics, dramatically reduce the artifacts related to cell shapes and overcome the difficulties of simulating anisotropic molecules under constant hydrostatic pressure or constant volume. The methods are especially effective for anisotropic liquids, such as smectic liquid crystals and membranes, of which the stacks of layers are compressible (elastic in direction perpendicular to the layers) while the layer itself is liquid and only elastic under uniform compressive force. The methods can also be used for crystals and isotropic liquids as well.
Molecular Dynamics Simulations of Alpha-synuclein
NASA Astrophysics Data System (ADS)
Sammalkorpi, Maria; Schreck, Carl; Nath, Abhinav; Dewitt, David; Rhoades, Elizabeth; O'Hern, Corey
2011-03-01
We investigate the conformational dynamics of single alpha-synuclein proteins, which have been implicated in amyloid diseases such as Parkinson's and Alzheimer's disease, in solution using unconstrained and constrained all-atom, explicit solvent molecular dynamics simulations. The constraints on inter-residue separations are obtained from our single-molecule FRET measurements of eleven FRET pairs that span the protein. By comparing the simulation data satisfying different combinations of FRET constraints, we are able to identify those constraints that are most important in determining the radius of gyration and key features of the contact map of the protein.
Bardhan, Jaydeep P.; Jungwirth, Pavel; Makowski, Lee
2012-01-01
Two mechanisms have been proposed to drive asymmetric solvent response to a solute charge: a static potential contribution similar to the liquid-vapor potential, and a steric contribution associated with a water molecule's structure and charge distribution. In this work, we use free-energy perturbation molecular-dynamics calculations in explicit water to show that these mechanisms act in complementary regimes; the large static potential (∼44 kJ/mol/e) dominates asymmetric response for deeply buried charges, and the steric contribution dominates for charges near the solute-solvent interface. Therefore, both mechanisms must be included in order to fully account for asymmetric solvation in general. Our calculations suggest that the steric contribution leads to a remarkable deviation from the popular “linear response” model in which the reaction potential changes linearly as a function of charge. In fact, the potential varies in a piecewise-linear fashion, i.e., with different proportionality constants depending on the sign of the charge. This discrepancy is significant even when the charge is completely buried, and holds for solutes larger than single atoms. Together, these mechanisms suggest that implicit-solvent models can be improved using a combination of affine response (an offset due to the static potential) and piecewise-linear response (due to the steric contribution). PMID:23020318
Molecular dynamics at constant Cauchy stress
NASA Astrophysics Data System (ADS)
Miller, Ronald E.; Tadmor, Ellad B.; Gibson, Joshua S.; Bernstein, Noam; Pavia, Fabio
2016-05-01
The Parrinello-Rahman algorithm for imposing a general state of stress in periodic molecular dynamics simulations is widely used in the literature and has been implemented in many readily available molecular dynamics codes. However, what is often overlooked is that this algorithm controls the second Piola-Kirchhoff stress as opposed to the true (Cauchy) stress. This can lead to misinterpretation of simulation results because (1) the true stress that is imposed during the simulation depends on the deformation of the periodic cell, (2) the true stress is potentially very different from the imposed second Piola-Kirchhoff stress, and (3) the true stress can vary significantly during the simulation even if the imposed second Piola-Kirchhoff is constant. We propose a simple modification to the algorithm that allows the true Cauchy stress to be controlled directly. We then demonstrate the efficacy of the new algorithm with the example of martensitic phase transformations under applied stress.
New faster CHARMM molecular dynamics engine
Hynninen, Antti-Pekka; Crowley, Michael F
2014-01-01
We introduce a new faster molecular dynamics (MD) engine into the CHARMM software package. The new MD engine is faster both in serial (i.e., single CPU core) and parallel execution. Serial performance is approximately two times higher than in the previous version of CHARMM. The newly programmed parallelization method allows the MD engine to parallelize up to hundreds of CPU cores. PMID:24302199
Nanoindentation of Zr by molecular dynamics simulation
NASA Astrophysics Data System (ADS)
Lu (芦子哲), Zizhe; Chernatynskiy, Aleksandr; Noordhoek, Mark J.; Sinnott, Susan B.; Phillpot, Simon R.
2015-12-01
Molecular dynamics simulations of nanoindentation are used to study the deformation behaviors of single crystal Zr for four different surface orientations. The comparison of results for two different potentials, an embedded atom method potential and a charged optimized many body potential, reveals the influence of stable and unstable stacking fault energy on dislocation behaviors under nanoindentation. The load-displacement curve, hardness and deformation behaviors of the various surface orientations Zr are compared and the elastic and plastic deformation behaviors are analyzed.
Molecular dynamics modelling of solidification in metals
Boercker, D.B.; Belak, J.; Glosli, J.
1997-12-31
Molecular dynamics modeling is used to study the solidification of metals at high pressure and temperature. Constant pressure MD is applied to a simulation cell initially filled with both solid and molten metal. The solid/liquid interface is tracked as a function of time, and the data are used to estimate growth rates of crystallites at high pressure and temperature in Ta and Mg.
Multiscale molecular dynamics using the matched interface and boundary method
Geng Weihua; Wei, G.W.
2011-01-20
The Poisson-Boltzmann (PB) equation is an established multiscale model for electrostatic analysis of biomolecules and other dielectric systems. PB based molecular dynamics (MD) approach has a potential to tackle large biological systems. Obstacles that hinder the current development of PB based MD methods are concerns in accuracy, stability, efficiency and reliability. The presence of complex solvent-solute interface, geometric singularities and charge singularities leads to challenges in the numerical solution of the PB equation and electrostatic force evaluation in PB based MD methods. Recently, the matched interface and boundary (MIB) method has been utilized to develop the first second order accurate PB solver that is numerically stable in dealing with discontinuous dielectric coefficients, complex geometric singularities and singular source charges. The present work develops the PB based MD approach using the MIB method. New formulation of electrostatic forces is derived to allow the use of sharp molecular surfaces. Accurate reaction field forces are obtained by directly differentiating the electrostatic potential. Dielectric boundary forces are evaluated at the solvent-solute interface using an accurate Cartesian-grid surface integration method. The electrostatic forces located at reentrant surfaces are appropriately assigned to related atoms. Extensive numerical tests are carried out to validate the accuracy and stability of the present electrostatic force calculation. The new PB based MD method is implemented in conjunction with the AMBER package. MIB based MD simulations of biomolecules are demonstrated via a few example systems.
Structure and dynamics of complex liquid water: Molecular dynamics simulation
NASA Astrophysics Data System (ADS)
S, Indrajith V.; Natesan, Baskaran
2015-06-01
We have carried out detailed structure and dynamical studies of complex liquid water using molecular dynamics simulations. Three different model potentials, namely, TIP3P, TIP4P and SPC-E have been used in the simulations, in order to arrive at the best possible potential function that could reproduce the structure of experimental bulk water. All the simulations were performed in the NVE micro canonical ensemble using LAMMPS. The radial distribution functions, gOO, gOH and gHH and the self diffusion coefficient, Ds, were calculated for all three models. We conclude from our results that the structure and dynamical parameters obtained for SPC-E model matched well with the experimental values, suggesting that among the models studied here, the SPC-E model gives the best structure and dynamics of bulk water.
Molecular crowding and protein enzymatic dynamics.
Echeverria, Carlos; Kapral, Raymond
2012-05-21
The effects of molecular crowding on the enzymatic conformational dynamics and transport properties of adenylate kinase are investigated. This tridomain protein undergoes large scale hinge motions in the course of its enzymatic cycle and serves as prototype for the study of crowding effects on the cyclic conformational dynamics of proteins. The study is carried out at a mesoscopic level where both the protein and the solvent in which it is dissolved are treated in a coarse grained fashion. The amino acid residues in the protein are represented by a network of beads and the solvent dynamics is described by multiparticle collision dynamics that includes effects due to hydrodynamic interactions. The system is crowded by a stationary random array of hard spherical objects. Protein enzymatic dynamics is investigated as a function of the obstacle volume fraction and size. In addition, for comparison, results are presented for a modification of the dynamics that suppresses hydrodynamic interactions. Consistent with expectations, simulations of the dynamics show that the protein prefers a closed conformation for high volume fractions. This effect becomes more pronounced as the obstacle radius decreases for a given volume fraction since the average void size in the obstacle array is smaller for smaller radii. At high volume fractions for small obstacle radii, the average enzymatic cycle time and characteristic times of internal conformational motions of the protein deviate substantially from their values in solution or in systems with small density of obstacles. The transport properties of the protein are strongly affected by molecular crowding. Diffusive motion adopts a subdiffusive character and the effective diffusion coefficients can change by more than an order of magnitude. The orientational relaxation time of the protein is also significantly altered by crowding. PMID:22476233
NASA Astrophysics Data System (ADS)
Tao, Jianmin; Rappe, Andrew M.
2016-01-01
Due to the absence of the long-range van der Waals (vdW) interaction, conventional density functional theory (DFT) often fails in the description of molecular complexes and solids. In recent years, considerable progress has been made in the development of the vdW correction. However, the vdW correction based on the leading-order coefficient C6 alone can only achieve limited accuracy, while accurate modeling of higher-order coefficients remains a formidable task, due to the strong non-additivity effect. Here, we apply a model dynamic multipole polarizability within a modified single-frequency approximation to calculate C8 and C10 between small molecules. We find that the higher-order vdW coefficients from this model can achieve remarkable accuracy, with mean absolute relative deviations of 5% for C8 and 7% for C10. Inclusion of accurate higher-order contributions in the vdW correction will effectively enhance the predictive power of DFT in condensed matter physics and quantum chemistry.
Frontiers in molecular dynamics simulations of DNA.
Pérez, Alberto; Luque, F Javier; Orozco, Modesto
2012-02-21
It has been known for decades that DNA is extremely flexible and polymorphic, but our knowledge of its accessible conformational space remains limited. Structural data, primarily from X-ray diffraction studies, is sparse in comparison to the manifold configurations possible, and direct experimental examinations of DNA's flexibility still suffer from many limitations. In the face of these shortcomings, molecular dynamics (MD) is now an essential tool in the study of DNA. It affords detailed structural and dynamical insights, which explains its recent transition from a small number of highly specialized laboratories to a large variety of groups dealing with challenging biological problems. MD is now making an irreversible journey to the mainstream of research in biology, with the attendant opportunities and challenges. But given the speed with which MD studies of DNA have spread, the roots remain somewhat shallow: in many cases, there is a lack of deep knowledge about the foundations, strengths, and limits of the technique. In this Account, we discuss how MD has become the most important source of structural and flexibility data on DNA, focusing on advances since 2007 of atomistic MD in the description of DNA under near-physiological conditions and highlighting the possibilities and shortcomings of the technique. The evolution in the field over the past four years is a prelude to the ongoing revolution. The technique has gained in robustness and predictive power, which when coupled with the spectacular improvements in software and hardware has enabled the tackling of systems of increasing complexity. Simulation times of microseconds have now been achieved, with even longer times when specialized hardware is used. As a result, we have seen the first real-time simulation of large conformational transitions, including folding and unfolding of short DNA duplexes. Noteworthy advances have also been made in the study of DNA-ligand interactions, and we predict that a global
Control-volume representation of molecular dynamics.
Smith, E R; Heyes, D M; Dini, D; Zaki, T A
2012-05-01
A molecular dynamics (MD) parallel to the control volume (CV) formulation of fluid mechanics is developed by integrating the formulas of Irving and Kirkwood [J. Chem. Phys. 18, 817 (1950)] over a finite cubic volume of molecular dimensions. The Lagrangian molecular system is expressed in terms of an Eulerian CV, which yields an equivalent to Reynolds' transport theorem for the discrete system. This approach casts the dynamics of the molecular system into a form that can be readily compared to the continuum equations. The MD equations of motion are reinterpreted in terms of a Lagrangian-to-control-volume (LCV) conversion function ϑ(i) for each molecule i. The LCV function and its spatial derivatives are used to express fluxes and relevant forces across the control surfaces. The relationship between the local pressures computed using the volume average [Lutsko, J. Appl. Phys. 64, 1152 (1988)] techniques and the method of planes [Todd et al., Phys. Rev. E 52, 1627 (1995)] emerges naturally from the treatment. Numerical experiments using the MD CV method are reported for equilibrium and nonequilibrium (start-up Couette flow) model liquids, which demonstrate the advantages of the formulation. The CV formulation of the MD is shown to be exactly conservative and is, therefore, ideally suited to obtain macroscopic properties from a discrete system.
Control-volume representation of molecular dynamics
NASA Astrophysics Data System (ADS)
Smith, E. R.; Heyes, D. M.; Dini, D.; Zaki, T. A.
2012-05-01
A molecular dynamics (MD) parallel to the control volume (CV) formulation of fluid mechanics is developed by integrating the formulas of Irving and Kirkwood [J. Chem. Phys.JCPSA60021-960610.1063/1.1747782 18, 817 (1950)] over a finite cubic volume of molecular dimensions. The Lagrangian molecular system is expressed in terms of an Eulerian CV, which yields an equivalent to Reynolds’ transport theorem for the discrete system. This approach casts the dynamics of the molecular system into a form that can be readily compared to the continuum equations. The MD equations of motion are reinterpreted in terms of a Lagrangian-to-control-volume (LCV) conversion function ϑi for each molecule i. The LCV function and its spatial derivatives are used to express fluxes and relevant forces across the control surfaces. The relationship between the local pressures computed using the volume average [Lutsko, J. Appl. Phys.JAPIAU0021-897910.1063/1.341877 64, 1152 (1988)] techniques and the method of planes [Todd , Phys. Rev. EPLEEE81539-375510.1103/PhysRevE.52.1627 52, 1627 (1995)] emerges naturally from the treatment. Numerical experiments using the MD CV method are reported for equilibrium and nonequilibrium (start-up Couette flow) model liquids, which demonstrate the advantages of the formulation. The CV formulation of the MD is shown to be exactly conservative and is, therefore, ideally suited to obtain macroscopic properties from a discrete system.
High temperature phonon dispersion in graphene using classical molecular dynamics
Anees, P. Panigrahi, B. K.; Valsakumar, M. C.
2014-04-24
Phonon dispersion and phonon density of states of graphene are calculated using classical molecular dynamics simulations. In this method, the dynamical matrix is constructed based on linear response theory by computing the displacement of atoms during the simulations. The computed phonon dispersions show excellent agreement with experiments. The simulations are done in both NVT and NPT ensembles at 300 K and found that the LO/TO modes are getting hardened at the Γ point. The NPT ensemble simulations capture the anharmonicity of the crystal accurately and the hardening of LO/TO modes is more pronounced. We also found that at 300 K the C-C bond length reduces below the equilibrium value and the ZA bending mode frequency becomes imaginary close to Γ along K-Γ direction, which indicates instability of the flat 2D graphene sheets.
Molecular dynamics simulation study of methanesulfonic acid.
Canales, Manel; Alemán, Carlos
2014-03-27
A molecular dynamics simulation study of methanesulfonic acid has been carried out using a reliable force field in a large range of temperatures. Several thermodynamic, structural, and dynamical properties have been calculated and compared with the available experimental data. The density, the shear viscosity, the heat of vaporization, and the melting temperature results, calculated from this force field, are in a good agreement with the experimental data. Analysis of the influence of the hydrogen bonds in structural and dynamical properties has also been performed. The continuous and interrupted methodologies to compute hydrogen bonding lifetimes have been applied. The interrupted hydrogen bond lifetimes values are consistent with the diffusion and viscosity coefficients. The activation energies of the self-diffusion, the reorientational motions, and the hydrogen bonding lifetimes are coincident.
Polymer Fluid Dynamics: Continuum and Molecular Approaches.
Bird, R B; Giacomin, A J
2016-06-01
To solve problems in polymer fluid dynamics, one needs the equations of continuity, motion, and energy. The last two equations contain the stress tensor and the heat-flux vector for the material. There are two ways to formulate the stress tensor: (a) One can write a continuum expression for the stress tensor in terms of kinematic tensors, or (b) one can select a molecular model that represents the polymer molecule and then develop an expression for the stress tensor from kinetic theory. The advantage of the kinetic theory approach is that one gets information about the relation between the molecular structure of the polymers and the rheological properties. We restrict the discussion primarily to the simplest stress tensor expressions or constitutive equations containing from two to four adjustable parameters, although we do indicate how these formulations may be extended to give more complicated expressions. We also explore how these simplest expressions are recovered as special cases of a more general framework, the Oldroyd 8-constant model. Studying the simplest models allows us to discover which types of empiricisms or molecular models seem to be worth investigating further. We also explore equivalences between continuum and molecular approaches. We restrict the discussion to several types of simple flows, such as shearing flows and extensional flows, which are of greatest importance in industrial operations. Furthermore, if these simple flows cannot be well described by continuum or molecular models, then it is not necessary to lavish time and energy to apply them to more complex flow problems. PMID:27276553
Application of optimal prediction to molecular dynamics
Barber, IV, John Letherman
2004-12-01
Optimal prediction is a general system reduction technique for large sets of differential equations. In this method, which was devised by Chorin, Hald, Kast, Kupferman, and Levy, a projection operator formalism is used to construct a smaller system of equations governing the dynamics of a subset of the original degrees of freedom. This reduced system consists of an effective Hamiltonian dynamics, augmented by an integral memory term and a random noise term. Molecular dynamics is a method for simulating large systems of interacting fluid particles. In this thesis, I construct a formalism for applying optimal prediction to molecular dynamics, producing reduced systems from which the properties of the original system can be recovered. These reduced systems require significantly less computational time than the original system. I initially consider first-order optimal prediction, in which the memory and noise terms are neglected. I construct a pair approximation to the renormalized potential, and ignore three-particle and higher interactions. This produces a reduced system that correctly reproduces static properties of the original system, such as energy and pressure, at low-to-moderate densities. However, it fails to capture dynamical quantities, such as autocorrelation functions. I next derive a short-memory approximation, in which the memory term is represented as a linear frictional force with configuration-dependent coefficients. This allows the use of a Fokker-Planck equation to show that, in this regime, the noise is δ-correlated in time. This linear friction model reproduces not only the static properties of the original system, but also the autocorrelation functions of dynamical variables.
Numerical methods for molecular dynamics. Progress report
Skeel, R.D.
1991-12-31
This report summarizes our research progress to date on the use of multigrid methods for three-dimensional elliptic partial differential equations, with particular emphasis on application to the Poisson-Boltzmann equation of molecular biophysics. This research is motivated by the need for fast and accurate numerical solution techniques for three-dimensional problems arising in physics and engineering. In many applications these problems must be solved repeatedly, and the extremely large number of discrete unknowns required to accurately approximate solutions to partial differential equations in three-dimensional regions necessitates the use of efficient solution methods. This situation makes clear the importance of developing methods which are of optimal order (or nearly so), meaning that the number of operations required to solve the discrete problem is on the order of the number of discrete unknowns. Multigrid methods are generally regarded as being in this class of methods, and are in fact provably optimal order for an increasingly large class of problems. The fundamental goal of this research is to develop a fast and accurate numerical technique, based on multi-level principles, for the solutions of the Poisson-Boltzmann equation of molecular biophysics and similar equations occurring in other applications. An outline of the report is as follows. We first present some background material, followed by a survey of the literature on the use of multigrid methods for solving problems similar to the Poisson-Boltzmann equation. A short description of the software we have developed so far is then given, and numerical results are discussed. Finally, our research plans for the coming year are presented.
5D model for accurate representation and visualization of dynamic cardiac structures
NASA Astrophysics Data System (ADS)
Lin, Wei-te; Robb, Richard A.
2000-05-01
Accurate cardiac modeling is challenging due to the intricate structure and complex contraction patterns of myocardial tissues. Fast imaging techniques can provide 4D structural information acquired as a sequence of 3D images throughout the cardiac cycle. To mode. The beating heart, we created a physics-based surface model that deforms between successive time point in the cardiac cycle. 3D images of canine hearts were acquired during one complete cardiac cycle using the DSR and the EBCT. The left ventricle of the first time point is reconstructed as a triangular mesh. A mass-spring physics-based deformable mode,, which can expand and shrink with local contraction and stretching forces distributed in an anatomically accurate simulation of cardiac motion, is applied to the initial mesh and allows the initial mesh to deform to fit the left ventricle in successive time increments of the sequence. The resulting 4D model can be interactively transformed and displayed with associated regional electrical activity mapped onto anatomic surfaces, producing a 5D model, which faithfully exhibits regional cardiac contraction and relaxation patterns over the entire heart. The model faithfully represents structural changes throughout the cardiac cycle. Such models provide the framework for minimizing the number of time points required to usefully depict regional motion of myocardium and allow quantitative assessment of regional myocardial motion. The electrical activation mapping provides spatial and temporal correlation within the cardiac cycle. In procedures which as intra-cardiac catheter ablation, visualization of the dynamic model can be used to accurately localize the foci of myocardial arrhythmias and guide positioning of catheters for optimal ablation.
Monitoring of cache miss rates for accurate dynamic voltage and frequency scaling
NASA Astrophysics Data System (ADS)
Singleton, Leo C.; Poellabauer, Christian; Schwan, Karsten
2005-01-01
Modern mobile processors offer dynamic voltage and frequency scaling, which can be used to reduce the energy requirements of embedded and real-time applications by exploiting idle CPU resources, while still maintaining all applications' real-time characteristics. However, accurate predictions of task run-times are key to computing the frequencies and voltages that ensure that all tasks' real-time constraints are met. Past work has used feedback-based approaches, where applications' past CPU utilizations are used to predict future CPU requirements. Inaccurate predictions in these approaches can lead to missed deadlines, less than expected energy savings, or large overheads due to frequent voltage and frequency changes. Previous solutions ignore other `indicators' of future CPU requirements, such as the frequency of I/O operations, memory accesses, or interrupts. This paper addresses this shortcoming for memory-intensive applications, where measured task run-times and cache miss rates are used as feedback for accurate run-time predictions. Cache miss rates indicate the frequency of memory accesses and enable us to derive the latencies introduced by these operations. The results shown in this paper indicate improvements in the number of deadlines met and the amount of energy saved.
Monitoring of cache miss rates for accurate dynamic voltage and frequency scaling
NASA Astrophysics Data System (ADS)
Singleton, Leo C.; Poellabauer, Christian; Schwan, Karsten
2004-12-01
Modern mobile processors offer dynamic voltage and frequency scaling, which can be used to reduce the energy requirements of embedded and real-time applications by exploiting idle CPU resources, while still maintaining all applications' real-time characteristics. However, accurate predictions of task run-times are key to computing the frequencies and voltages that ensure that all tasks' real-time constraints are met. Past work has used feedback-based approaches, where applications' past CPU utilizations are used to predict future CPU requirements. Inaccurate predictions in these approaches can lead to missed deadlines, less than expected energy savings, or large overheads due to frequent voltage and frequency changes. Previous solutions ignore other `indicators' of future CPU requirements, such as the frequency of I/O operations, memory accesses, or interrupts. This paper addresses this shortcoming for memory-intensive applications, where measured task run-times and cache miss rates are used as feedback for accurate run-time predictions. Cache miss rates indicate the frequency of memory accesses and enable us to derive the latencies introduced by these operations. The results shown in this paper indicate improvements in the number of deadlines met and the amount of energy saved.
Stochastic Event-Driven Molecular Dynamics
Donev, Aleksandar Garcia, Alejandro L.; Alder, Berni J.
2008-02-01
A novel Stochastic Event-Driven Molecular Dynamics (SEDMD) algorithm is developed for the simulation of polymer chains suspended in a solvent. SEDMD combines event-driven molecular dynamics (EDMD) with the Direct Simulation Monte Carlo (DSMC) method. The polymers are represented as chains of hard-spheres tethered by square wells and interact with the solvent particles with hard-core potentials. The algorithm uses EDMD for the simulation of the polymer chain and the interactions between the chain beads and the surrounding solvent particles. The interactions between the solvent particles themselves are not treated deterministically as in EDMD, rather, the momentum and energy exchange in the solvent is determined stochastically using DSMC. The coupling between the solvent and the solute is consistently represented at the particle level retaining hydrodynamic interactions and thermodynamic fluctuations. However, unlike full MD simulations of both the solvent and the solute, in SEDMD the spatial structure of the solvent is ignored. The SEDMD algorithm is described in detail and applied to the study of the dynamics of a polymer chain tethered to a hard-wall subjected to uniform shear. SEDMD closely reproduces results obtained using traditional EDMD simulations with two orders of magnitude greater efficiency. Results question the existence of periodic (cycling) motion of the polymer chain.
Molecular dynamics in high electric fields
NASA Astrophysics Data System (ADS)
Apostol, M.; Cune, L. C.
2016-06-01
Molecular rotation spectra, generated by the coupling of the molecular electric-dipole moments to an external time-dependent electric field, are discussed in a few particular conditions which can be of some experimental interest. First, the spherical-pendulum molecular model is reviewed, with the aim of introducing an approximate method which consists in the separation of the azimuthal and zenithal motions. Second, rotation spectra are considered in the presence of a static electric field. Two particular cases are analyzed, corresponding to strong and weak fields. In both cases the classical motion of the dipoles consists of rotations and vibrations about equilibrium positions; this motion may exhibit parametric resonances. For strong fields a large macroscopic electric polarization may appear. This situation may be relevant for polar matter (like pyroelectrics, ferroelectrics), or for heavy impurities embedded in a polar solid. The dipolar interaction is analyzed in polar condensed matter, where it is shown that new polarization modes appear for a spontaneous macroscopic electric polarization (these modes are tentatively called "dipolons"); one of the polarization modes is related to parametric resonances. The extension of these considerations to magnetic dipoles is briefly discussed. The treatment is extended to strong electric fields which oscillate with a high frequency, as those provided by high-power lasers. It is shown that the effect of such fields on molecular dynamics is governed by a much weaker, effective, renormalized, static electric field.
Molecular Dynamics: New Frontier in Personalized Medicine.
Sneha, P; Doss, C George Priya
2016-01-01
The field of drug discovery has witnessed infinite development over the last decade with the demand for discovery of novel efficient lead compounds. Although the development of novel compounds in this field has seen large failure, a breakthrough in this area might be the establishment of personalized medicine. The trend of personalized medicine has shown stupendous growth being a hot topic after the successful completion of Human Genome Project and 1000 genomes pilot project. Genomic variant such as SNPs play a vital role with respect to inter individual's disease susceptibility and drug response. Hence, identification of such genetic variants has to be performed before administration of a drug. This process requires high-end techniques to understand the complexity of the molecules which might bring an insight to understand the compounds at their molecular level. To sustenance this, field of bioinformatics plays a crucial role in revealing the molecular mechanism of the mutation and thereby designing a drug for an individual in fast and affordable manner. High-end computational methods, such as molecular dynamics (MD) simulation has proved to be a constitutive approach to detecting the minor changes associated with an SNP for better understanding of the structural and functional relationship. The parameters used in molecular dynamic simulation elucidate different properties of a macromolecule, such as protein stability and flexibility. MD along with docking analysis can reveal the synergetic effect of an SNP in protein-ligand interaction and provides a foundation for designing a particular drug molecule for an individual. This compelling application of computational power and the advent of other technologies have paved a promising way toward personalized medicine. In this in-depth review, we tried to highlight the different wings of MD toward personalized medicine. PMID:26827606
Molecular Dynamics: New Frontier in Personalized Medicine.
Sneha, P; Doss, C George Priya
2016-01-01
The field of drug discovery has witnessed infinite development over the last decade with the demand for discovery of novel efficient lead compounds. Although the development of novel compounds in this field has seen large failure, a breakthrough in this area might be the establishment of personalized medicine. The trend of personalized medicine has shown stupendous growth being a hot topic after the successful completion of Human Genome Project and 1000 genomes pilot project. Genomic variant such as SNPs play a vital role with respect to inter individual's disease susceptibility and drug response. Hence, identification of such genetic variants has to be performed before administration of a drug. This process requires high-end techniques to understand the complexity of the molecules which might bring an insight to understand the compounds at their molecular level. To sustenance this, field of bioinformatics plays a crucial role in revealing the molecular mechanism of the mutation and thereby designing a drug for an individual in fast and affordable manner. High-end computational methods, such as molecular dynamics (MD) simulation has proved to be a constitutive approach to detecting the minor changes associated with an SNP for better understanding of the structural and functional relationship. The parameters used in molecular dynamic simulation elucidate different properties of a macromolecule, such as protein stability and flexibility. MD along with docking analysis can reveal the synergetic effect of an SNP in protein-ligand interaction and provides a foundation for designing a particular drug molecule for an individual. This compelling application of computational power and the advent of other technologies have paved a promising way toward personalized medicine. In this in-depth review, we tried to highlight the different wings of MD toward personalized medicine.
Hyperdynamics: Accelerated Molecular Dynamics of Infrequent Events
Voter, A.F.
1997-05-01
I derive a general method for accelerating the molecular-dynamics (MD) simulation of infrequent events in solids. A bias potential ({Delta}V{sub b}) raises the energy in regions other than the transition states between potential basins. Transitions occur at an accelerated rate and the elapsed time becomes a statistical property of the system. {Delta}V{sub b} can be constructed without knowing the location of the transition states and implementation requires only first derivatives. I examine the diffusion mechanisms of a 10-atom Ag cluster on the Ag(111) surface using a 220 {mu}s hyper-MD simulation. {copyright} {ital 1997} {ital The American Physical Society}
[Oligoglycine surface structures: molecular dynamics simulation].
Gus'kova, O A; Khalatur, P G; Khokhlov, A R; Chinarev, A A; Tsygankova, S V; Bovin, N V
2010-01-01
The full-atomic molecular dynamics (MD) simulation of adsorption mode for diantennary oligoglycines [H-Gly4-NH(CH2)5]2 onto graphite and mica surface is described. The resulting structure of adsorption layers is analyzed. The peptide second structure motives have been studied by both STRIDE (structural identification) and DSSP (dictionary of secondary structure of proteins) methods. The obtained results confirm the possibility of polyglycine II (PGII) structure formation in diantennary oligoglycine (DAOG) monolayers deposited onto graphite surface, which was earlier estimated based on atomic-force microscopy measurements.
Molecular dynamics simulation of ice XII
NASA Astrophysics Data System (ADS)
Borzsák, István; Cummings, Peter T.
1999-02-01
Molecular dynamics simulations have been performed on the newly discovered metastable ice XII. This new crystalline ice phase [C. Lobban, J.L. Finney, W.F. Kuhs, Nature (London) 391 (1998) 268] is proton-disordered. Thus 90 possible configurations of the unit cell can be constructed which differ only in the orientations of the water molecules. The simulation used the TIP4P potential model for water at constant temperature and density. About one-quarter of the initial configurations did not melt in the course of the simulation. This result is supportive of the experimental structure and also demonstrates the ability of this water model to study ice phases.
Crystallization of nickel nanoclusters by molecular dynamics
NASA Astrophysics Data System (ADS)
Chamati, H.; Gaminchev, K.
2012-12-01
We investigated the melting properties of bulk nickel and the crystallization of nickel nanocrystals via molecular dynamics using a potential in the framework of the second moment approximation of tight-binding theory. The melting behavior was simulated with the hysteresis approach by subsequently heating and cooling gradually the system over a wide range of temperatures. The crystallization of nickel nanoclusters consisting of 55, 147 and 309 atoms was achieved after repeatedly annealing and quenching the corresponding quasicrystals several times to avoid being trapped in a local energy minimum. The time over which the global minimum was reached was found to increase with the cluster size.
Quinci, Federico; Dressler, Matthew; Strickland, Anthony M; Limbert, Georges
2014-04-01
Considerable progress has been made in understanding implant wear and developing numerical models to predict wear for new orthopaedic devices. However any model of wear could be improved through a more accurate representation of the biomaterial mechanics, including time-varying dynamic and inelastic behaviour such as viscosity and plastic deformation. In particular, most computational models of wear of UHMWPE implement a time-invariant version of Archard's law that links the volume of worn material to the contact pressure between the metal implant and the polymeric tibial insert. During in-vivo conditions, however, the contact area is a time-varying quantity and is therefore dependent upon the dynamic deformation response of the material. From this observation one can conclude that creep deformations of UHMWPE may be very important to consider when conducting computational wear analyses, in stark contrast to what can be found in the literature. In this study, different numerical modelling techniques are compared with experimental creep testing on a unicondylar knee replacement system in a physiologically representative context. Linear elastic, plastic and time-varying visco-dynamic models are benchmarked using literature data to predict contact deformations, pressures and areas. The aim of this study is to elucidate the contributions of viscoelastic and plastic effects on these surface quantities. It is concluded that creep deformations have a significant effect on the contact pressure measured (experiment) and calculated (computational models) at the surface of the UHMWPE unicondylar insert. The use of a purely elastoplastic constitutive model for UHMWPE lead to compressive deformations of the insert which are much smaller than those predicted by a creep-capturing viscoelastic model (and those measured experimentally). This shows again the importance of including creep behaviour into a constitutive model in order to predict the right level of surface deformation
Quinci, Federico; Dressler, Matthew; Strickland, Anthony M; Limbert, Georges
2014-04-01
Considerable progress has been made in understanding implant wear and developing numerical models to predict wear for new orthopaedic devices. However any model of wear could be improved through a more accurate representation of the biomaterial mechanics, including time-varying dynamic and inelastic behaviour such as viscosity and plastic deformation. In particular, most computational models of wear of UHMWPE implement a time-invariant version of Archard's law that links the volume of worn material to the contact pressure between the metal implant and the polymeric tibial insert. During in-vivo conditions, however, the contact area is a time-varying quantity and is therefore dependent upon the dynamic deformation response of the material. From this observation one can conclude that creep deformations of UHMWPE may be very important to consider when conducting computational wear analyses, in stark contrast to what can be found in the literature. In this study, different numerical modelling techniques are compared with experimental creep testing on a unicondylar knee replacement system in a physiologically representative context. Linear elastic, plastic and time-varying visco-dynamic models are benchmarked using literature data to predict contact deformations, pressures and areas. The aim of this study is to elucidate the contributions of viscoelastic and plastic effects on these surface quantities. It is concluded that creep deformations have a significant effect on the contact pressure measured (experiment) and calculated (computational models) at the surface of the UHMWPE unicondylar insert. The use of a purely elastoplastic constitutive model for UHMWPE lead to compressive deformations of the insert which are much smaller than those predicted by a creep-capturing viscoelastic model (and those measured experimentally). This shows again the importance of including creep behaviour into a constitutive model in order to predict the right level of surface deformation
Combining Molecular Dynamics and Density Functional Theory
NASA Astrophysics Data System (ADS)
Kaxiras, Efthimios
2015-03-01
The time evolution of a system consisting of electrons and ions is often treated in the Born-Oppenheimer approximation, with electrons in their instantaneous ground state. This approach cannot capture many interesting processes that involved excitation of electrons and its effects on the coupled electron-ion dynamics. The time scale needed to accurately resolve the evolution of electron dynamics is atto-seconds. This poses a challenge to the simulation of important chemical processes that typically take place on time scales of pico-seconds and beyond, such as reactions at surfaces and charge transport in macromolecules. We will present a methodology based on time-dependent density functional theory for electrons, and classical (Ehrenfest) dynamics for the ions, that successfully captures such processes. We will give a review of key features of the method and several applications. These illustrate how the atomic and electronic structure evolution unravels the elementary steps that constitute a chemical reaction. In collaboration with: G. Kolesov, D. Vinichenko, G. Tritsaris, C.M. Friend, Departments of Physics and of Chemistry and Chemical Biology.
Steered Molecular Dynamics Methods Applied to Enzyme Mechanism and Energetics.
Ramírez, C L; Martí, M A; Roitberg, A E
2016-01-01
One of the main goals of chemistry is to understand the underlying principles of chemical reactions, in terms of both its reaction mechanism and the thermodynamics that govern it. Using hybrid quantum mechanics/molecular mechanics (QM/MM)-based methods in combination with a biased sampling scheme, it is possible to simulate chemical reactions occurring inside complex environments such as an enzyme, or aqueous solution, and determining the corresponding free energy profile, which provides direct comparison with experimental determined kinetic and equilibrium parameters. Among the most promising biasing schemes is the multiple steered molecular dynamics method, which in combination with Jarzynski's Relationship (JR) allows obtaining the equilibrium free energy profile, from a finite set of nonequilibrium reactive trajectories by exponentially averaging the individual work profiles. However, obtaining statistically converged and accurate profiles is far from easy and may result in increased computational cost if the selected steering speed and number of trajectories are inappropriately chosen. In this small review, using the extensively studied chorismate to prephenate conversion reaction, we first present a systematic study of how key parameters such as pulling speed, number of trajectories, and reaction progress are related to the resulting work distributions and in turn the accuracy of the free energy obtained with JR. Second, and in the context of QM/MM strategies, we introduce the Hybrid Differential Relaxation Algorithm, and show how it allows obtaining more accurate free energy profiles using faster pulling speeds and smaller number of trajectories and thus smaller computational cost.
Steered Molecular Dynamics Methods Applied to Enzyme Mechanism and Energetics.
Ramírez, C L; Martí, M A; Roitberg, A E
2016-01-01
One of the main goals of chemistry is to understand the underlying principles of chemical reactions, in terms of both its reaction mechanism and the thermodynamics that govern it. Using hybrid quantum mechanics/molecular mechanics (QM/MM)-based methods in combination with a biased sampling scheme, it is possible to simulate chemical reactions occurring inside complex environments such as an enzyme, or aqueous solution, and determining the corresponding free energy profile, which provides direct comparison with experimental determined kinetic and equilibrium parameters. Among the most promising biasing schemes is the multiple steered molecular dynamics method, which in combination with Jarzynski's Relationship (JR) allows obtaining the equilibrium free energy profile, from a finite set of nonequilibrium reactive trajectories by exponentially averaging the individual work profiles. However, obtaining statistically converged and accurate profiles is far from easy and may result in increased computational cost if the selected steering speed and number of trajectories are inappropriately chosen. In this small review, using the extensively studied chorismate to prephenate conversion reaction, we first present a systematic study of how key parameters such as pulling speed, number of trajectories, and reaction progress are related to the resulting work distributions and in turn the accuracy of the free energy obtained with JR. Second, and in the context of QM/MM strategies, we introduce the Hybrid Differential Relaxation Algorithm, and show how it allows obtaining more accurate free energy profiles using faster pulling speeds and smaller number of trajectories and thus smaller computational cost. PMID:27497165
An Efficient Time-Stepping Scheme for Ab Initio Molecular Dynamics Simulations
NASA Astrophysics Data System (ADS)
Tsuchida, Eiji
2016-08-01
In ab initio molecular dynamics simulations of real-world problems, the simple Verlet method is still widely used for integrating the equations of motion, while more efficient algorithms are routinely used in classical molecular dynamics. We show that if the Verlet method is used in conjunction with pre- and postprocessing, the accuracy of the time integration is significantly improved with only a small computational overhead. We also propose several extensions of the algorithm required for use in ab initio molecular dynamics. The validity of the processed Verlet method is demonstrated in several examples including ab initio molecular dynamics simulations of liquid water. The structural properties obtained from the processed Verlet method are found to be sufficiently accurate even for large time steps close to the stability limit. This approach results in a 2× performance gain over the standard Verlet method for a given accuracy. We also show how to generate a canonical ensemble within this approach.
Exact dynamic properties of molecular motors
NASA Astrophysics Data System (ADS)
Boon, N. J.; Hoyle, R. B.
2012-08-01
Molecular motors play important roles within a biological cell, performing functions such as intracellular transport and gene transcription. Recent experimental work suggests that there are many plausible biochemical mechanisms that molecules such as myosin-V could use to achieve motion. To account for the abundance of possible discrete-stochastic frameworks that can arise when modeling molecular motor walks, a generalized and straightforward graphical method for calculating their dynamic properties is presented. It allows the calculation of the velocity, dispersion, and randomness ratio for any proposed system through analysis of its structure. This article extends work of King and Altman ["A schematic method of deriving the rate laws of enzyme-catalyzed reactions," J. Phys. Chem. 60, 1375-1378 (1956)], 10.1021/j150544a010 on networks of enzymatic reactions by calculating additional dynamic properties for spatially hopping systems. Results for n-state systems are presented: single chain, parallel pathway, divided pathway, and divided pathway with a chain. A novel technique for combining multiple system architectures coupled at a reference state is also demonstrated. Four-state examples illustrate the effectiveness and simplicity of these methods.
MDLab: a molecular dynamics simulation prototyping environment.
Cickovski, Trevor; Chatterjee, Santanu; Wenger, Jacob; Sweet, Christopher R; Izaguirre, Jesús A
2010-05-01
Molecular dynamics (MD) simulation involves solving Newton's equations of motion for a system of atoms, by calculating forces and updating atomic positions and velocities over a timestep Deltat. Despite the large amount of computing power currently available, the timescale of MD simulations is limited by both the small timestep required for propagation, and the expensive algorithm for computing pairwise forces. These issues are currently addressed through the development of efficient simulation methods, some of which make acceptable approximations and as a result can afford larger timesteps. We present MDLab, a development environment for MD simulations built with Python which facilitates prototyping, testing, and debugging of these methods. MDLab provides constructs which allow the development of propagators, force calculators, and high level sampling protocols that run several instances of molecular dynamics. For computationally demanding sampling protocols which require testing on large biomolecules, MDL includes an interface to the OpenMM libraries of Friedrichs et al. which execute on graphical processing units (GPUs) and achieve considerable speedup over execution on the CPU. As an example of an interesting high level method developed in MDLab, we present a parallel implementation of the On-The-Fly string method of Maragliano and Vanden-Eijnden. MDLab is available at http://mdlab.sourceforge.net.
Molecular dynamics of the excitatory synapse.
Okabe, Shigeo
2012-01-01
Molecular dynamics of synapses are one of the most important factors that control the remodeling of synaptic connection and efficacy of transmission. This chapter focuses on the dynamics of postsynaptic molecular machinery and describes the imaging technologies important for quantitative analyses of synapses, their application to the postsynaptic molecules, and the insights obtained from these analyses. New visualization techniques, such as super-resolution microscopy, will become an indispensable approach to reveal submicron changes of synaptic molecules. New methods of monitoring protein interactions will also be integrated with experimental paradigms of synaptic plasticity. Cell biological analyses, together with cutting-edge imaging technologies, have been applied to the studies of nascent synapse formation, synapse maintenance, and activity-dependent synapse remodeling. From these studies, a variety of new concepts emerged, such as local assembly of postsynaptic scaffolds, presence of "transport packets" of postsynaptic receptors, heterogeneity of actin movement within spines, and activity-free fluctuation of PSD/spine sizes. These new concepts are useful in understanding specific properties of postsynaptic functions and should be integrated in future to build a realistic model of the postsynaptic organization that can explain its remarkable stability and tunability. PMID:22351054
Structure and Dynamics of Cellulose Molecular Solutions
NASA Astrophysics Data System (ADS)
Wang, Howard; Zhang, Xin; Tyagi, Madhusudan; Mao, Yimin; Briber, Robert
Molecular dissolution of microcrystalline cellulose has been achieved through mixing with ionic liquid 1-Ethyl-3-methylimidazolium acetate (EMIMAc), and organic solvent dimethylformamide (DMF). The mechanism of cellulose dissolution in tertiary mixtures has been investigated by combining quasielastic and small angle neutron scattering (QENS and SANS). As SANS data show that cellulose chains take Gaussian-like conformations in homogenous solutions, which exhibit characteristics of having an upper critical solution temperature, the dynamic signals predominantly from EMIMAc molecules indicate strong association with cellulose in the dissolution state. The mean square displacement quantities support the observation of the stoichiometric 3:1 EMIMAc to cellulose unit molar ratio, which is a necessary criterion for the molecular dissolution of cellulose. Analyses of dynamics structure factors reveal the temperature dependence of a slow and a fast process for EMIMAc's bound to cellulose and in DMF, respectively, as well as a very fast process due possibly to the rotational motion of methyl groups, which persisted to near the absolute zero.
NASA Astrophysics Data System (ADS)
Pagliai, Marco; Muniz-Miranda, Maurizio; Cardini, Gianni; Schettino, Vincenzo
2011-05-01
Ab initio molecular dynamics simulations with the Car-Parrinello method have been performed on the spodumene crystal at standard conditions and high pressure. Starting from the computed trajectories, accurate Raman and infrared spectra have been obtained and compared with available experimental measurements in the low and high pressure phases. The structural and spectroscopic changes due to the pressure effects are discussed.
Size effects in molecular dynamics thermal conductivity predictions
NASA Astrophysics Data System (ADS)
Sellan, D. P.; Landry, E. S.; Turney, J. E.; McGaughey, A. J. H.; Amon, C. H.
2010-06-01
We predict the bulk thermal conductivity of Lennard-Jones argon and Stillinger-Weber silicon using the Green-Kubo (GK) and direct methods in classical molecular dynamics simulations. While system-size-independent thermal conductivities can be obtained with less than 1000 atoms for both materials using the GK method, the linear extrapolation procedure [Schelling , Phys. Rev. B 65, 144306 (2002)] must be applied to direct method results for multiple system sizes. We find that applying the linear extrapolation procedure in a manner consistent with previous researchers can lead to an underprediction of the GK thermal conductivity (e.g., by a factor of 2.5 for Stillinger-Weber silicon at a temperature of 500 K). To understand this discrepancy, we perform lattice dynamics calculations to predict phonon properties and from these, length-dependent thermal conductivities. From these results, we find that the linear extrapolation procedure is only accurate when the minimum system size used in the direct method simulations is comparable to the largest mean-free paths of the phonons that dominate the thermal transport. This condition has not typically been satisfied in previous works. To aid in future studies, we present a simple metric for determining if the system sizes used in direct method simulations are sufficiently large so that the linear extrapolation procedure can accurately predict the bulk thermal conductivity.
Dynamic transitions in molecular dynamics simulations of supercooled silicon
NASA Astrophysics Data System (ADS)
Mei, Xiaojun; Eapen, Jacob
2013-04-01
Two dynamic transitions or crossovers, one at a low temperature (T* ≈ 1006 K) and the other at a high temperature (T0 ≈ 1384 K), are shown to emerge in supercooled liquid silicon using molecular dynamics simulations. The high-temperature transition (T0) marks the decoupling of stress, density, and energy relaxation mechanisms. At the low-temperature transition (T*), depending on the cooling rate, supercooled silicon can either undergo a high-density-liquid to low-density-liquid (HDL-LDL) phase transition or experience an HDL-HDL crossover. Dynamically heterogeneous domains that emerge with supercooling become prominent across the HDL-HDL transition at 1006 K, with well-separated mobile and immobile regions. Interestingly, across the HDL-LDL transition, the most mobile atoms form large prominent aggregates while the least mobile atoms get spatially dispersed akin to that in a crystalline state. The attendant partial return to spatial uniformity with the HDL-LDL phase transition indicates a dynamic mechanism for relieving the frustration in supercooled states.
The 2011 Dynamics of Molecular Collisions Conference
Nesbitt, David J.
2011-07-11
The Dynamics of Molecular Collisions Conference focuses on all aspects of molecular collisions--experimental & theoretical studies of elastic, inelastic, & reactive encounters involving atoms, molecules, ions, clusters, & surfaces--as well as half collisions--photodissociation, photo-induced reaction, & photodesorption. The scientific program for the meeting in 2011 included exciting advances in both the core & multidisciplinary forefronts of the study of molecular collision processes. Following the format of the 2009 meeting, we also invited sessions in special topics that involve interfacial dynamics, novel emerging spectroscopies, chemical dynamics in atmospheric, combustion & interstellar environments, as well as a session devoted to theoretical & experimental advances in ultracold molecular samples. Researchers working inside & outside the traditional core topics of the meeting are encouraged to join the conference. We invite contributions of work that seeks understanding of how inter & intra-molecular forces determine the dynamics of the phenomena under study. In addition to invited oral sessions & contributed poster sessions, the scientific program included a formal session consisting of five contributed talks selected from the submitted poster abstracts. The DMC has distinguished itself by having the Herschbach Medal Symposium as part of the meeting format. This tradition of the Herschbach Medal was first started in the 2007 meeting chaired by David Chandler, based on a generous donation of funds & artwork design by Professor Dudley Herschbach himself. There are two such awards made, one for experimental & one for theoretical contributions to the field of Molecular Collision Dynamics, broadly defined. The symposium is always held on the last night of the meeting & has the awardees are asked to deliver an invited lecture on their work. The 2011 Herschbach Medal was dedicated to the contributions of two long standing leaders in Chemical Physics, Professor
Molecular dynamics simulations of wear processes
NASA Astrophysics Data System (ADS)
Yu, Hualiang
Wear has been recognized as a vital problem in many industries. It results in a loss of durability, reliability, and efficiency and costs tens of billions of dollars annually. Significant effort has been devoted in both experimental and theoretical studies. However, the mechanisms of wear are still poorly understood and therefore wear control is far behind its demand. One way to study wear process is via computer simulation, which has become more powerful with the rapid development in computer facilities and efficient algorithms. It allows observation of atomic scale deformation and therefore it is a very good tool to study wear mechanisms at the nano-scale. This study presents a series of molecular dynamic simulation of some nano-scale wear processes, such as indentation and plowing, with the goal of exploring the factors that affect wear and predicting wear for different conditions. Molecular Dynamics simulations were carried out on a system that includes an aluminum substrate and a hard tip. Embedded atom method (EAM) and Lennard-Jones potentials were used to describe interactions between atoms. For nano-indentation simulations, both constant indent force and constant loading speed were applied to study the wear mechanisms as well as material properties. Some phenomenon, such as jump-to-contact, local melting, and dislocation nucleation were observed. More importantly, the effects of system temperature, indent force, substrate orientation, tip-substrate bond, indenter shape, boundary condition, and defect concentrations of the substrate were systematically investigated during indentation. The results are in qualitative agreement with limited experimental data. Similar simulations were carried out for plowing. The effects of plowing force, substrate orientation, the tip-substrate bond, and alloy elements are discussed based on the simulation results. In addition, a simple analytic model of plowing behavior is provided. The model reveals two parameters, static
Molecular dynamics simulations of uniaxial deformation of thermoplastic polyimides.
Nazarychev, V M; Lyulin, A V; Larin, S V; Gurtovenko, A A; Kenny, J M; Lyulin, S V
2016-05-01
The results of atomistic molecular-dynamics simulations of mechanical properties of heterocyclic polymer subjected to uniaxial deformation are reported. A new amorphous thermoplastic polyimide R-BAPO with a repeat unit consisting of dianhydride 1,3-bis-(3',4,-dicarboxyphenoxy)diphenyl (dianhydride R) and diamine 4,4'-bis-(4''-aminophenoxy)diphenyloxide (diamine BAPO) was chosen for the simulations. Our primary goal was to establish the impact of various factors (sample preparation method, molecular mass, and cooling and deformation rates) on the elasticity modulus. In particular, we found that the elasticity modulus was only slightly affected by the degree of equilibration, the molecular mass and the size of the simulation box. This is most likely due to the fact that the main contribution to the elasticity modulus is from processes on scales smaller than the entanglement length. Essentially, our simulations reproduce the logarithmic dependence of the elasticity modulus on cooling and deformation rates, which is normally observed in experiments. With the use of the temperature dependence analysis of the elasticity modulus we determined the flow temperature of R-BAPO to be 580 K in line with the experimental data available. Furthermore, we found that the application of high external pressure to the polymer sample during uniaxial deformation can improve the mechanical properties of the polyimide. Overall, the results of our simulations clearly demonstrate that atomistic molecular-dynamics simulations represent a powerful and accurate tool for studying the mechanical properties of heterocyclic polymers and can therefore be useful for the virtual design of new materials, thereby supporting cost-effective synthesis and experimental research. PMID:27033967
Detecting Allosteric Networks Using Molecular Dynamics Simulation.
Bowerman, S; Wereszczynski, J
2016-01-01
Allosteric networks allow enzymes to transmit information and regulate their catalytic activities over vast distances. In principle, molecular dynamics (MD) simulations can be used to reveal the mechanisms that underlie this phenomenon; in practice, it can be difficult to discern allosteric signals from MD trajectories. Here, we describe how MD simulations can be analyzed to reveal correlated motions and allosteric networks, and provide an example of their use on the coagulation enzyme thrombin. Methods are discussed for calculating residue-pair correlations from atomic fluctuations and mutual information, which can be combined with contact information to identify allosteric networks and to dynamically cluster a system into highly correlated communities. In the case of thrombin, these methods show that binding of the antagonist hirugen significantly alters the enzyme's correlation landscape through a series of pathways between Exosite I and the catalytic core. Results suggest that hirugen binding curtails dynamic diversity and enforces stricter venues of influence, thus reducing the accessibility of thrombin to other molecules. PMID:27497176
The Relation between Approximation in Distribution and Shadowing in Molecular Dynamics
NASA Astrophysics Data System (ADS)
Tupper, Paul
2009-01-01
Molecular dynamics refers to the computer simulation of a material at the atomic level. An open problem in numerical analysis is to explain the apparent reliability of molecular dynamics simulations. The difficulty is that individual trajectories computed in molecular dynamics are accurate for only short time intervals, whereas apparently reliable information can be extracted from very long-time simulations. It has been conjectured that long molecular dynamics trajectories have low-dimensional statistical features that accurately approximate those of the original system. Another conjecture is that numerical trajectories satisfy the shadowing property: they are close over long time intervals to exact trajectories but with different initial conditions. We prove that these two views are actually equivalent to each other, after we suitably modify the concept of shadowing. A key ingredient of our result is a general theorem that allows us to take random elements of a metric space that are close in distribution and embed them in the same probability space so that they are close in a strong sense. This result is similar to the Strassen-Dudley theorem except that a mapping is provided between the two random elements. Our results on shadowing are motivated by molecular dynamics but apply to the approximation of any dynamical system when initial conditions are selected according to a probability measure.
Ion motions in molecular dynamics simulations on DNA
NASA Astrophysics Data System (ADS)
Ponomarev, Sergei Y.; Thayer, Kelly M.; Beveridge, David L.
2004-10-01
Counterions play a significant role in DNA structure and function, and molecular dynamics (MD) simulations offer the prospect of detailed description of the dynamical structure of ions at the molecular level. However, the motions of mobile counterions are notably slow to converge in MD on DNA. Obtaining accurate and reliable MD simulations requires knowing just how much sampling is required for convergence of each of the properties of interest. To address this issue, MD on a d(CGCGAATTCGCG) duplex in a dilute aqueous solution of water and 22 Na+ counterions was performed until convergence was achieved. The calculated first shell ion occupancies and DNA-Na+ radial distribution functions were computed as a function of time to assess convergence, and compared with relaxation times of the DNA internal parameters shift, slide, rise, tilt, roll, and twist. The sequence dependence of fractional occupancies of ions in the major and minor grooves of the DNA is examined, and the possibility of correlation between ion proximity and DNA minor groove widths is investigated.
Role of Molecular Dynamics and Related Methods in Drug Discovery.
De Vivo, Marco; Masetti, Matteo; Bottegoni, Giovanni; Cavalli, Andrea
2016-05-12
Molecular dynamics (MD) and related methods are close to becoming routine computational tools for drug discovery. Their main advantage is in explicitly treating structural flexibility and entropic effects. This allows a more accurate estimate of the thermodynamics and kinetics associated with drug-target recognition and binding, as better algorithms and hardware architectures increase their use. Here, we review the theoretical background of MD and enhanced sampling methods, focusing on free-energy perturbation, metadynamics, steered MD, and other methods most consistently used to study drug-target binding. We discuss unbiased MD simulations that nowadays allow the observation of unsupervised ligand-target binding, assessing how these approaches help optimizing target affinity and drug residence time toward improved drug efficacy. Further issues discussed include allosteric modulation and the role of water molecules in ligand binding and optimization. We conclude by calling for more prospective studies to attest to these methods' utility in discovering novel drug candidates. PMID:26807648
Molecular dynamics of shock loading of metals with defects
Belak, J.F.
1997-12-31
The finite rise time of shock waves in metals is commonly attributed to dissipative or viscous behavior of the metal. This viscous or plastic behavior is commonly attributed to the motion of defects such as dislocations. Despite this intuitive understanding, the experimental observation of defect motion or nucleation during shock loading has not been possible due to the short time scales involved. Molecular dynamics modeling with realistic interatomic potentials can provide some insight into defect motion during shock loading. However, until quite recently, the length scale required to accurately represent a metal with defects has been beyond the scope of even the most powerful supercomputers. Here, the author presents simulations of the shock response of single defects and indicate how simulation might provide some insight into the shock loading of metals.
Nguyen, Thuy-Diem; Schmidt, Bertil; Zheng, Zejun; Kwoh, Chee-Keong
2015-01-01
De novo clustering is a popular technique to perform taxonomic profiling of a microbial community by grouping 16S rRNA amplicon reads into operational taxonomic units (OTUs). In this work, we introduce a new dendrogram-based OTU clustering pipeline called CRiSPy. The key idea used in CRiSPy to improve clustering accuracy is the application of an anomaly detection technique to obtain a dynamic distance cutoff instead of using the de facto value of 97 percent sequence similarity as in most existing OTU clustering pipelines. This technique works by detecting an abrupt change in the merging heights of a dendrogram. To produce the output dendrograms, CRiSPy employs the OTU hierarchical clustering approach that is computed on a genetic distance matrix derived from an all-against-all read comparison by pairwise sequence alignment. However, most existing dendrogram-based tools have difficulty processing datasets larger than 10,000 unique reads due to high computational complexity. We address this difficulty by developing two efficient algorithms for CRiSPy: a compute-efficient GPU-accelerated parallel algorithm for pairwise distance matrix computation and a memory-efficient hierarchical clustering algorithm. Our experiments on various datasets with distinct attributes show that CRiSPy is able to produce more accurate OTU groupings than most OTU clustering applications. PMID:26451819
Aeroacoustic Flow Phenomena Accurately Captured by New Computational Fluid Dynamics Method
NASA Technical Reports Server (NTRS)
Blech, Richard A.
2002-01-01
One of the challenges in the computational fluid dynamics area is the accurate calculation of aeroacoustic phenomena, especially in the presence of shock waves. One such phenomenon is "transonic resonance," where an unsteady shock wave at the throat of a convergent-divergent nozzle results in the emission of acoustic tones. The space-time Conservation-Element and Solution-Element (CE/SE) method developed at the NASA Glenn Research Center can faithfully capture the shock waves, their unsteady motion, and the generated acoustic tones. The CE/SE method is a revolutionary new approach to the numerical modeling of physical phenomena where features with steep gradients (e.g., shock waves, phase transition, etc.) must coexist with those having weaker variations. The CE/SE method does not require the complex interpolation procedures (that allow for the possibility of a shock between grid cells) used by many other methods to transfer information between grid cells. These interpolation procedures can add too much numerical dissipation to the solution process. Thus, while shocks are resolved, weaker waves, such as acoustic waves, are washed out.
Osmosis : a molecular dynamics computer simulation study
NASA Astrophysics Data System (ADS)
Lion, Thomas
Osmosis is a phenomenon of critical importance in a variety of processes ranging from the transport of ions across cell membranes and the regulation of blood salt levels by the kidneys to the desalination of water and the production of clean energy using potential osmotic power plants. However, despite its importance and over one hundred years of study, there is an ongoing confusion concerning the nature of the microscopic dynamics of the solvent particles in their transfer across the membrane. In this thesis the microscopic dynamical processes underlying osmotic pressure and concentration gradients are investigated using molecular dynamics (MD) simulations. I first present a new derivation for the local pressure that can be used for determining osmotic pressure gradients. Using this result, the steady-state osmotic pressure is studied in a minimal model for an osmotic system and the steady-state density gradients are explained using a simple mechanistic hopping model for the solvent particles. The simulation setup is then modified, allowing us to explore the timescales involved in the relaxation dynamics of the system in the period preceding the steady state. Further consideration is also given to the relative roles of diffusive and non-diffusive solvent transport in this period. Finally, in a novel modification to the classic osmosis experiment, the solute particles are driven out-of-equilibrium by the input of energy. The effect of this modification on the osmotic pressure and the osmotic ow is studied and we find that active solute particles can cause reverse osmosis to occur. The possibility of defining a new "osmotic effective temperature" is also considered and compared to the results of diffusive and kinetic temperatures..
Accurate determination of the nuclear quadrupole moment of xenon from the molecular method
NASA Astrophysics Data System (ADS)
Canella, Guilherme A.; Santiago, Régis T.; Haiduke, Roberto L. A.
2016-09-01
This study provides a new determination of the nuclear electric quadrupole moment (NQM) for 131Xe, which is achieved by the molecular method. Dirac-Coulomb Coupled Cluster calculations with a Gaunt correction (DC+G-CC) of electric field gradients (EFGs) and experimental nuclear quadrupole coupling constants of six molecular systems (XeH+, XeCuF, XeCuCl, XeAgF, XeAgCl and XeAuF) were considered. The best NQM obtained by our DC+G-CCSD-T EFGs was -114.6(1.1) mbarn, which is recommended as the new reference value for this nuclide given the high level electron structure calculations done here.
Fiber lubrication: A molecular dynamics simulation study
NASA Astrophysics Data System (ADS)
Liu, Hongyi
Molecular and mesoscopic level description of friction and lubrication remains a challenge because of difficulties in the phenomenological understanding of to the behaviors of solid-liquid interfaces during sliding. Fortunately, there is the computational simulation approach opens an opportunity to predict and analyze interfacial phenomena, which were studied with molecular dynamics (MD) and mesoscopic dynamics (MesoDyn) simulations. Polypropylene (PP) and cellulose are two of most common polymers in textile fibers. Confined amorphous surface layers of PP and cellulose were built successfully with xenon crystals which were used to compact the polymers. The physical and surface properties of the PP and cellulose surface layers were investigated by MD simulations, including the density, cohesive energy, volumetric thermal expansion, and contact angle with water. The topology method was employed to predict the properties of poly(alkylene glycol) (PAG) diblock copolymers and Pluronic triblock copolymers used as lubricants on surfaces. Density, zero shear viscosity, shear module, cohesive energy and solubility parameter were predicted with each block copolymer. Molecular dynamics simulations were used to study the interaction energy per unit contact area of block copolymer melts with PP and cellulose surfaces. The interaction energy is defined as the ratio of interfacial interaction energy to the contact area. Both poly(proplene oxide) (PPO) and poly(ethylene oxide) (PEO) segments provided a lipophilic character to both PP and cellulose surfaces. The PPO/PEO ratio and the molecular weight were found to impact the interaction energy on both PP and cellulose surfaces. In aqueous solutions, the interaction energy is complicated due to the presence of water and the cross interactions between the multiple molecular components. The polymer-water-surface (PWS) calculation method was proposed to calculate such complex systems. In a contrast with a vacuum condition, the presence
Development of semiclassical molecular dynamics simulation method.
Nakamura, Hiroki; Nanbu, Shinkoh; Teranishi, Yoshiaki; Ohta, Ayumi
2016-04-28
Various quantum mechanical effects such as nonadiabatic transitions, quantum mechanical tunneling and coherence play crucial roles in a variety of chemical and biological systems. In this paper, we propose a method to incorporate tunneling effects into the molecular dynamics (MD) method, which is purely based on classical mechanics. Caustics, which define the boundary between classically allowed and forbidden regions, are detected along classical trajectories and the optimal tunneling path with minimum action is determined by starting from each appropriate caustic. The real phase associated with tunneling can also be estimated. Numerical demonstration with use of a simple collinear chemical reaction O + HCl → OH + Cl is presented in order to help the reader to well comprehend the method proposed here. Generalization to the on-the-fly ab initio version is rather straightforward. By treating the nonadiabatic transitions at conical intersections by the Zhu-Nakamura theory, new semiclassical MD methods can be developed. PMID:27067383
Nonequilibrium molecular dynamics: The first 25 years
Hoover, W.G. |
1992-08-01
Equilibrium Molecular Dynamics has been generalized to simulate Nonequilibrium systems by adding sources of thermodynamic heat and work. This generalization incorporates microscopic mechanical definitions of macroscopic thermodynamic and hydrodynamic variables, such as temperature and stress, and augments atomistic forces with special boundary, constraint, and driving forces capable of doing work on, and exchanging heat with, an otherwise Newtonian system. The underlying Lyapunov instability of these nonequilibrium equations of motion links microscopic time-reversible deterministic trajectories to macroscopic time-irreversible hydrodynamic behavior as described by the Second Law of Thermodynamics. Green-Kubo linear-response theory has been checked. Nonlinear plastic deformation, intense heat conduction, shockwave propagation, and nonequilibrium phase transformation have all been simulated. The nonequilibrium techniques, coupled with qualitative improvements in parallel computer hardware, are enabling simulations to approximate real-world microscale and nanoscale experiments.
Classical Molecular Dynamics Simulation of Nuclear Fuel
Devanathan, Ram; Krack, Matthias; Bertolus, Marjorie
2015-10-10
Molecular dynamics simulation is well suited to study primary damage production by irradiation, defect interactions with fission gas atoms, gas bubble nucleation, grain boundary effects on defect and gas bubble evolution in nuclear fuel, and the resulting changes in thermo-mechanical properties. In these simulations, the forces on the ions are dictated by interaction potentials generated by fitting properties of interest to experimental data. The results obtained from the present generation of potentials are qualitatively similar, but quantitatively different. There is a need to refine existing potentials to provide a better representation of the performance of polycrystalline fuel under a variety of operating conditions, and to develop models that are equipped to handle deviations from stoichiometry. In addition to providing insights into fundamental mechanisms governing the behaviour of nuclear fuel, MD simulations can also provide parameters that can be used as inputs for mesoscale models.
Molecular Dynamics Studies of Gold Surfaces
NASA Astrophysics Data System (ADS)
Ercolessi, F.; Bartolini, A.; Garofalo, M.; Parrinello, M.; Tosatti, E.
1987-01-01
In the glue model the total cohesion of a metal is determined by a pairwise atom-atom effective interaction plus a many-body force (the "glue") which is introduced to ensure optimal coordination. Using parameters optimized for gold, we have studied the structural behaviour of the low index surfaces Au(100), Au(110) and Au(111). We have used a simulated annealing strategy based on molecular dynamics to search the lowest surface energy configuration. In all cases the optimal structures are found to be reconstructed, and remarkably similar to some experimentally suggested reconstruction models. The main driving mechanism is the formation of close-packed triangular surface layers favoured by the glue term.
Extended Lagrangian free energy molecular dynamics.
Niklasson, Anders M N; Steneteg, Peter; Bock, Nicolas
2011-10-28
Extended free energy Lagrangians are proposed for first principles molecular dynamics simulations at finite electronic temperatures for plane-wave pseudopotential and local orbital density matrix-based calculations. Thanks to the extended Lagrangian description, the electronic degrees of freedom can be integrated by stable geometric schemes that conserve the free energy. For the local orbital representations both the nuclear and electronic forces have simple and numerically efficient expressions that are well suited for reduced complexity calculations. A rapidly converging recursive Fermi operator expansion method that does not require the calculation of eigenvalues and eigenfunctions for the construction of the fractionally occupied density matrix is discussed. An efficient expression for the Pulay force that is valid also for density matrices with fractional occupation occurring at finite electronic temperatures is also demonstrated.
Development of semiclassical molecular dynamics simulation method.
Nakamura, Hiroki; Nanbu, Shinkoh; Teranishi, Yoshiaki; Ohta, Ayumi
2016-04-28
Various quantum mechanical effects such as nonadiabatic transitions, quantum mechanical tunneling and coherence play crucial roles in a variety of chemical and biological systems. In this paper, we propose a method to incorporate tunneling effects into the molecular dynamics (MD) method, which is purely based on classical mechanics. Caustics, which define the boundary between classically allowed and forbidden regions, are detected along classical trajectories and the optimal tunneling path with minimum action is determined by starting from each appropriate caustic. The real phase associated with tunneling can also be estimated. Numerical demonstration with use of a simple collinear chemical reaction O + HCl → OH + Cl is presented in order to help the reader to well comprehend the method proposed here. Generalization to the on-the-fly ab initio version is rather straightforward. By treating the nonadiabatic transitions at conical intersections by the Zhu-Nakamura theory, new semiclassical MD methods can be developed.
Nonequilibrium molecular dynamics of liquid crystals
NASA Astrophysics Data System (ADS)
Sarman, S. S.; Cummings, P. T.; Evans, D. J.
1994-11-01
During the last 15 years, noneyuilibrium molecular dynamics (NEMD) has been successfully applied to study transport phenomena in fluids that are isotropic at equilibrium. A natural extension is therefore to study liquid crystals, which are anisotropic al equilibrium. The lower symmetry of these systems means that the linear transport coefficients are considerably more complicated than in an isotropic system. Part of the reason for this is that there are crosscouplings between tensors of different rank and parity. Such couplings arc symmetry-forbidden in isotropic phases. In this paper. we review some of fundamental theoretical results we have derived concerning the rheology of liquid crystals. report NEMD simulations of thermal conductivity and shear viscosity of liquid crystals, and present NEMD simulations of shear cessation phenomena. All of the NEMD results are presented for a model liquid crystal fluid which is a modification of the Gay-Borne fluid. The results obtained are in qualitative agreement with experimental measurements on liquid crystal systems.
Assessing Molecular Dynamics Simulations with Solvatochromism Modeling.
Schwabe, Tobias
2015-08-20
For the modeling of solvatochromism with an explicit representation of the solvent molecules, the quality of preceding molecular dynamics simulations is crucial. Therefore, the possibility to apply force fields which are derived with as little empiricism as possible seems desirable. Such an approach is tested here by exploiting the sensitive solvatochromism of p-nitroaniline, and the use of reliable excitation energies based on approximate second-order coupled cluster results within a polarizable embedding scheme. The quality of the various MD settings for four different solvents, water, methanol, ethanol, and dichloromethane, is assessed. In general, good agreement with the experiment is observed when polarizable force fields and special treatment of hydrogen bonding are applied. PMID:26220273
Molecular dynamics studies of metallic glasses
NASA Astrophysics Data System (ADS)
Lee, Hyon-Jee
The thermodynamic, structural, and mechanical properties of metallic glasses are studied using molecular dynamics simulations. Molecular dynamics provides a computational framework to simulate the movement of interacting atoms in response to external perturbations, such as changes in temperature or pressure. In this thesis, a Sutton-Chen potential was chosen to describe the many-body interactions in metals and alloys. Our first application for this approach is to develop a simple model to derive the thermodynamic properties of metallic alloys (Chapter 2). Based on this model, we demonstrate that the glass transition is thermodynamically sensitive to differences between atomic radii and that there is an optimal difference for glass formation. Next, we extend these simulations to elucidate the details of structural organization in the glass (Chapter 3). We find that the liquid phase is characterized by a local five-fold symmetry, which becomes more prominent as the glass phase forms. This five-fold symmetry is related to the formation of icosahedral structures. The mechanical properties of glasses are also investigated and it is found that shear localization, which accompanies a sharp drop in the stress-strain curve, occurs at 45 degree with respect to the loading axis (Chapter 4). The generation of free volume is found to be the dominant mechanism that leads to shear localization, rather than adiabatic heating. Finally, generic first principle potentials are constructed to guide the experimental development of AlTiNi based metallic glasses (Chapter 5). Together, the results from these simulations improve our understanding of the thermodynamic, structural, and mechanical properties of metallic glasses and will aid computer-driven materials design.
Molecular dynamics simulations of microscale fluid transport
Wong, C.C.; Lopez, A.R.; Stevens, M.J.; Plimpton, S.J.
1998-02-01
Recent advances in micro-science and technology, like Micro-Electro-Mechanical Systems (MEMS), have generated a group of unique liquid flow problems that involve characteristic length scales of a Micron. Also, in manufacturing processes such as coatings, current continuum models are unable to predict microscale physical phenomena that appear in these non-equilibrium systems. It is suspected that in these systems, molecular-level processes can control the interfacial energy and viscoelastic properties at the liquid/solid boundary. A massively parallel molecular dynamics (MD) code has been developed to better understand microscale transport mechanisms, fluid-structure interactions, and scale effects in micro-domains. Specifically, this MD code has been used to analyze liquid channel flow problems for a variety of channel widths, e.g. 0.005-0.05 microns. This report presents results from MD simulations of Poiseuille flow and Couette flow problems and addresses both scaling and modeling issues. For Poiseuille flow, the numerical predictions are compared with existing data to investigate the variation of the friction factor with channel width. For Couette flow, the numerical predictions are used to determine the degree of slip at the liquid/solid boundary. Finally, the results also indicate that shear direction with respect to the wall lattice orientation can be very important. Simulation results of microscale Couette flow and microscale Poiseuille flow for two different surface structures and two different shear directions will be presented.
Molecular dynamics simulations of supramolecular polymer rheology
NASA Astrophysics Data System (ADS)
Li, Zhenlong; Djohari, Hadrian; Dormidontova, Elena E.
2010-11-01
Using equilibrium and nonequilibrium molecular dynamics simulations, we studied the equilibrium and rheological properties of dilute and semidilute solutions of head-to-tail associating polymers. In our simulation model, a spontaneous complementary reversible association between the donor and the acceptor groups at the ends of oligomers was achieved by introducing a combination of truncated pseudo-Coulombic attractive potential and Lennard Jones repulsive potential between donor, acceptor, and neighboring groups. We have calculated the equilibrium properties of supramolecular polymers, such as the ring/chain equilibrium, average molecular weight, and molecular weight distribution of self-assembled chains and rings, which all agree well with previous analytical and computer modeling results. We have investigated shear thinning of solutions of 8- and 20-bead associating oligomers with different association energies at different temperatures and oligomer volume fractions. All reduced viscosity data for a given oligomer length can be collapsed into one master curve, exhibiting two power-law regions of shear-thinning behavior with an exponent of -0.55 at intermediate ranges of the reduced shear rate β and -0.8 (or -0.9) at larger shear rates. The equilibrium viscosity of supramolecular solutions with different oligomer lengths and associating energies is found to obey a power-law scaling dependence on oligomer volume fraction with an exponent of 1.5, in agreement with the experimental observations for several dilute or semidilute solutions of supramolecular polymers. This implies that dilute and semidilute supramolecular polymer solutions exhibit high polydispersity but may not be sufficiently entangled to follow the reptation mechanism of relaxation.
Molecular beam studies of reaction dynamics
Lee, Y.T.
1993-12-01
The major thrust of this research project is to elucidate detailed dynamics of simple elementary reactions that are theoretically important and to unravel the mechanism of complex chemical reactions or photochemical processes that play important roles in many macroscopic processes. Molecular beams of reactants are used to study individual reactive encounters between molecules or to monitor photodissociation events in a collision-free environment. Most of the information is derived from measurement of the product fragment energy, angular, and state distributions. Recent activities are centered on the mechanisms of elementary chemical reactions involving oxygen atoms with unsaturated hydrocarbons, the dynamics of endothermic substitution reactions, the dependence of the chemical reactivity of electronically excited atoms on the alignment of excited orbitals, the primary photochemical processes of polyatomic molecules, intramolecular energy transfer of chemically activated and locally excited molecules, the energetics of free radicals that are important to combustion processes, the infrared-absorption spectra of carbonium ions and hydrated hydronium ions, and bond-selective photodissociation through electric excitation.
Molecular-dynamic study of liquid ethylenediamine
NASA Astrophysics Data System (ADS)
Balabaev, N. K.; Kraevskii, S. V.; Rodnikova, M. N.; Solonina, I. A.
2016-10-01
Models of liquid ethylenediamine (ED) are built using the molecular dynamics approach at temperatures of 293-363 K and a size of 1000 molecules in a basic cell as a cuboid. The structural and dynamic characteristics of liquid ED versus temperature are derived. The gauche conformation of the ED molecule that is characteristic of the gas phase is shown to transition easily into the trans conformation of the molecules in the liquid. NH···N hydrogen bonds are analyzed in liquid ED. The number of H-bonds per ED molecule is found to vary from 5.02 at 293 K to 3.86 at 363 K. The lifetimes in the range of the temperatures and dissociation activation energy for several H-bonds in liquid ED are found to range from 0.574 to 4.524 ps at 293 K; the activation energies are 8.8 kJ/mol for 50% of the H-bonds and 16.3 kJ/mol for 6.25% of them. A weaker and more mobile spatial grid of H-bonds in liquid ED is observed, compared to data calculated earlier for monoethanolamine.
Accelerated electronic structure-based molecular dynamics simulations of shock-induced chemistry
NASA Astrophysics Data System (ADS)
Cawkwell, Marc
2015-06-01
The initiation and progression of shock-induced chemistry in organic materials at moderate temperatures and pressures are slow on the time scales available to regular molecular dynamics simulations. Accessing the requisite time scales is particularly challenging if the interatomic bonding is modeled using accurate yet expensive methods based explicitly on electronic structure. We have combined fast, energy conserving extended Lagrangian Born-Oppenheimer molecular dynamics with the parallel replica accelerated molecular dynamics formalism to study the relatively sluggish shock-induced chemistry of benzene around 13-20 GPa. We model interatomic bonding in hydrocarbons using self-consistent tight binding theory with an accurate and transferable parameterization. Shock compression and its associated transient, non-equilibrium effects are captured explicitly by combining the universal liquid Hugoniot with a simple shrinking-cell boundary condition. A number of novel methods for improving the performance of reactive electronic structure-based molecular dynamics by adapting the self-consistent field procedure on-the-fly will also be discussed. The use of accelerated molecular dynamics has enabled us to follow the initial stages of the nucleation and growth of carbon clusters in benzene under thermodynamic conditions pertinent to experiments.
Molecular dynamics studies on nanoscale gas transport
NASA Astrophysics Data System (ADS)
Barisik, Murat
Three-dimensional molecular dynamics (MD) simulations of nanoscale gas flows are studied to reveal surface effects. A smart wall model that drastically reduces the memory requirements of MD simulations for gas flows is introduced. The smart wall molecular dynamics (SWMD) represents three-dimensional FCC walls using only 74 wall Molecules. This structure is kept in the memory and utilized for each gas molecule surface collision. Using SWMD, fluid behavior within nano-scale confinements is studied for argon in dilute gas, dense gas, and liquid states. Equilibrium MD method is employed to resolve the density and stress variations within the static fluid. Normal stress calculations are based on the Irving-Kirkwood method, which divides the stress tensor into its kinetic and virial parts. The kinetic component recovers pressure based on the ideal gas law. The particle-particle virial increases with increased density, while the surface-particle virial develops due to the surface force field effects. Normal stresses within nano-scale confinements show anisotropy induced primarily by the surface force-field and local variations in the fluid density near the surfaces. For dilute and dense gas cases, surface-force field that extends typically 1nm from each wall induces anisotropic normal stress. For liquid case, this effect is further amplified by the density fluctuations that extend beyond the three field penetration region. Outside the wall force-field penetration and density fluctuation regions the normal stress becomes isotropic and recovers the thermodynamic pressure, provided that sufficiently large force cut-off distances are utilized in the computations. Next, non-equilibrium SWMD is utilized to investigate the surface-gas interaction effects on nanoscale shear-driven gas flows in the transition and free molecular flow regimes. For the specified surface properties and gas-surface pair interactions, density and stress profiles exhibit a universal behavior inside the
Molecular Detection of Foodborne Pathogens: A Rapid and Accurate Answer to Food Safety.
Mangal, Manisha; Bansal, Sangita; Sharma, Satish K; Gupta, Ram K
2016-07-01
Food safety is a global health concern. For the prevention and recognition of problems related to health and safety, detection of foodborne pathogen is of utmost importance at all levels of food production chain. For several decades, a lot of research has been targeted at the development of rapid methodology as reducing the time needed to complete pathogen detection tests has been the primary goal of food microbiologists. With the result, food microbiology laboratories now have a wide array of detection methods and automated technologies such as enzyme immunoassay, polymerase chain reaction, and microarrays, which can cut test times considerably. Nucleic acid amplification strategies and advances in amplicon detection methodologies have been the key factors in the progress of molecular microbiology. A comprehensive literature survey has been carried out to give an overview in the field of foodborne pathogen detection. In this paper, we describe the conventional methods, as well as recent developments in food pathogen detection, identification, and quantification, with a major emphasis on molecular detection methods.
Internal Coordinate Molecular Dynamics: A Foundation for Multiscale Dynamics
2015-01-01
Internal coordinates such as bond lengths, bond angles, and torsion angles (BAT) are natural coordinates for describing a bonded molecular system. However, the molecular dynamics (MD) simulation methods that are widely used for proteins, DNA, and polymers are based on Cartesian coordinates owing to the mathematical simplicity of the equations of motion. However, constraints are often needed with Cartesian MD simulations to enhance the conformational sampling. This makes the equations of motion in the Cartesian coordinates differential-algebraic, which adversely impacts the complexity and the robustness of the simulations. On the other hand, constraints can be easily placed in BAT coordinates by removing the degrees of freedom that need to be constrained. Thus, the internal coordinate MD (ICMD) offers an attractive alternative to Cartesian coordinate MD for developing multiscale MD method. The torsional MD method is a special adaptation of the ICMD method, where all the bond lengths and bond angles are kept rigid. The advantages of ICMD simulation methods are the longer time step size afforded by freezing high frequency degrees of freedom and performing a conformational search in the more important low frequency torsional degrees of freedom. However, the advancements in the ICMD simulations have been slow and stifled by long-standing mathematical bottlenecks. In this review, we summarize the recent mathematical advancements we have made based on spatial operator algebra, in developing a robust long time scale ICMD simulation toolkit useful for various applications. We also present the applications of ICMD simulations to study conformational changes in proteins and protein structure refinement. We review the advantages of the ICMD simulations over the Cartesian simulations when used with enhanced sampling methods and project the future use of ICMD simulations in protein dynamics. PMID:25517406
In situ structure and dynamics of DNA origami determined through molecular dynamics simulations
Yoo, Jejoong; Aksimentiev, Aleksei
2013-01-01
The DNA origami method permits folding of long single-stranded DNA into complex 3D structures with subnanometer precision. Transmission electron microscopy, atomic force microscopy, and recently cryo-EM tomography have been used to characterize the properties of such DNA origami objects, however their microscopic structures and dynamics have remained unknown. Here, we report the results of all-atom molecular dynamics simulations that characterized the structural and mechanical properties of DNA origami objects in unprecedented microscopic detail. When simulated in an aqueous environment, the structures of DNA origami objects depart from their idealized targets as a result of steric, electrostatic, and solvent-mediated forces. Whereas the global structural features of such relaxed conformations conform to the target designs, local deformations are abundant and vary in magnitude along the structures. In contrast to their free-solution conformation, the Holliday junctions in the DNA origami structures adopt a left-handed antiparallel conformation. We find the DNA origami structures undergo considerable temporal fluctuations on both local and global scales. Analysis of such structural fluctuations reveals the local mechanical properties of the DNA origami objects. The lattice type of the structures considerably affects global mechanical properties such as bending rigidity. Our study demonstrates the potential of all-atom molecular dynamics simulations to play a considerable role in future development of the DNA origami field by providing accurate, quantitative assessment of local and global structural and mechanical properties of DNA origami objects. PMID:24277840
NASA Astrophysics Data System (ADS)
Hepburn, I.; Chen, W.; De Schutter, E.
2016-08-01
Spatial stochastic molecular simulations in biology are limited by the intense computation required to track molecules in space either in a discrete time or discrete space framework, which has led to the development of parallel methods that can take advantage of the power of modern supercomputers in recent years. We systematically test suggested components of stochastic reaction-diffusion operator splitting in the literature and discuss their effects on accuracy. We introduce an operator splitting implementation for irregular meshes that enhances accuracy with minimal performance cost. We test a range of models in small-scale MPI simulations from simple diffusion models to realistic biological models and find that multi-dimensional geometry partitioning is an important consideration for optimum performance. We demonstrate performance gains of 1-3 orders of magnitude in the parallel implementation, with peak performance strongly dependent on model specification.
Hepburn, I; Chen, W; De Schutter, E
2016-08-01
Spatial stochastic molecular simulations in biology are limited by the intense computation required to track molecules in space either in a discrete time or discrete space framework, which has led to the development of parallel methods that can take advantage of the power of modern supercomputers in recent years. We systematically test suggested components of stochastic reaction-diffusion operator splitting in the literature and discuss their effects on accuracy. We introduce an operator splitting implementation for irregular meshes that enhances accuracy with minimal performance cost. We test a range of models in small-scale MPI simulations from simple diffusion models to realistic biological models and find that multi-dimensional geometry partitioning is an important consideration for optimum performance. We demonstrate performance gains of 1-3 orders of magnitude in the parallel implementation, with peak performance strongly dependent on model specification. PMID:27497550
Hepburn, I; Chen, W; De Schutter, E
2016-08-01
Spatial stochastic molecular simulations in biology are limited by the intense computation required to track molecules in space either in a discrete time or discrete space framework, which has led to the development of parallel methods that can take advantage of the power of modern supercomputers in recent years. We systematically test suggested components of stochastic reaction-diffusion operator splitting in the literature and discuss their effects on accuracy. We introduce an operator splitting implementation for irregular meshes that enhances accuracy with minimal performance cost. We test a range of models in small-scale MPI simulations from simple diffusion models to realistic biological models and find that multi-dimensional geometry partitioning is an important consideration for optimum performance. We demonstrate performance gains of 1-3 orders of magnitude in the parallel implementation, with peak performance strongly dependent on model specification.
NASA Technical Reports Server (NTRS)
Boughner, Robert E.
1986-01-01
A method for calculating the photodissociation rates needed for photochemical modeling of the stratosphere, which includes the effects of molecular scattering, is described. The procedure is based on Sokolov's method of averaging functional correction. The radiation model and approximations used to calculate the radiation field are examined. The approximated diffuse fields and photolysis rates are compared with exact data. It is observed that the approximate solutions differ from the exact result by 10 percent or less at altitudes above 15 km; the photolysis rates differ from the exact rates by less than 5 percent for altitudes above 10 km and all zenith angles, and by less than 1 percent for altitudes above 15 km.
A new sensor system for accurate and precise determination of sediment dynamics and position.
NASA Astrophysics Data System (ADS)
Maniatis, Georgios; Hoey, Trevor; Sventek, Joseph; Hodge, Rebecca
2014-05-01
Sediment transport processes control many significant geomorphological changes. Consequently, sediment transport dynamics are studied across a wide range of scales leading to application of a variety of conceptually different mathematical descriptions (models) and data acquisition techniques (sensing). For river sediment transport processes both Eulerian and Lagrangian formulations are used. Data are gathered using a very wide range of sensing techniques that are not always compatible with the conceptual formulation applied. We are concerned with small to medium sediment grain-scale motion in gravel-bed rivers, and other coarse-grained environments, and: a) are developing a customised environmental sensor capable of providing coherent data that reliably record the motion; and, b) provide a mathematical framework in which these data can be analysed and interpreted, this being compatible with current stochastic approaches to sediment transport theory. Here we present results from three different aspects of the above developmental process. Firstly, we present a requirement analysis for the sensor based on the state of the art of the existing technologies. We focus on the factors that enhance data coherence and representativeness, extending the common practice for optimization which is based exclusively on electronics/computing related criteria. This analysis leads to formalization of a method that permits accurate control on the physical properties of the sensor using contemporary rapid prototyping techniques [Maniatis et al. 2013]. Secondly the first results are presented from a series of entrainment experiments in a 5 x 0.8 m flume in which a prototype sensor was deployed to monitor entrainment dynamics under increasing flow conditions (0.037 m3.s-1). The sensor was enclosed in an idealized spherical case (111 mm diameter) and placed on a constructed bed of hemispheres of the same diameter. We measured 3-axial inertial acceleration (as a measure of flow stress
Shen, Rong; Han, Wei; Fiorin, Giacomo; Islam, Shahidul M.; Schulten, Klaus; Roux, Benoît
2015-01-01
The knowledge of multiple conformational states is a prerequisite to understand the function of membrane transport proteins. Unfortunately, the determination of detailed atomic structures for all these functionally important conformational states with conventional high-resolution approaches is often difficult and unsuccessful. In some cases, biophysical and biochemical approaches can provide important complementary structural information that can be exploited with the help of advanced computational methods to derive structural models of specific conformational states. In particular, functional and spectroscopic measurements in combination with site-directed mutations constitute one important source of information to obtain these mixed-resolution structural models. A very common problem with this strategy, however, is the difficulty to simultaneously integrate all the information from multiple independent experiments involving different mutations or chemical labels to derive a unique structural model consistent with the data. To resolve this issue, a novel restrained molecular dynamics structural refinement method is developed to simultaneously incorporate multiple experimentally determined constraints (e.g., engineered metal bridges or spin-labels), each treated as an individual molecular fragment with all atomic details. The internal structure of each of the molecular fragments is treated realistically, while there is no interaction between different molecular fragments to avoid unphysical steric clashes. The information from all the molecular fragments is exploited simultaneously to constrain the backbone to refine a three-dimensional model of the conformational state of the protein. The method is illustrated by refining the structure of the voltage-sensing domain (VSD) of the Kv1.2 potassium channel in the resting state and by exploring the distance histograms between spin-labels attached to T4 lysozyme. The resulting VSD structures are in good agreement with
Shen, Rong; Han, Wei; Fiorin, Giacomo; Islam, Shahidul M; Schulten, Klaus; Roux, Benoît
2015-10-01
The knowledge of multiple conformational states is a prerequisite to understand the function of membrane transport proteins. Unfortunately, the determination of detailed atomic structures for all these functionally important conformational states with conventional high-resolution approaches is often difficult and unsuccessful. In some cases, biophysical and biochemical approaches can provide important complementary structural information that can be exploited with the help of advanced computational methods to derive structural models of specific conformational states. In particular, functional and spectroscopic measurements in combination with site-directed mutations constitute one important source of information to obtain these mixed-resolution structural models. A very common problem with this strategy, however, is the difficulty to simultaneously integrate all the information from multiple independent experiments involving different mutations or chemical labels to derive a unique structural model consistent with the data. To resolve this issue, a novel restrained molecular dynamics structural refinement method is developed to simultaneously incorporate multiple experimentally determined constraints (e.g., engineered metal bridges or spin-labels), each treated as an individual molecular fragment with all atomic details. The internal structure of each of the molecular fragments is treated realistically, while there is no interaction between different molecular fragments to avoid unphysical steric clashes. The information from all the molecular fragments is exploited simultaneously to constrain the backbone to refine a three-dimensional model of the conformational state of the protein. The method is illustrated by refining the structure of the voltage-sensing domain (VSD) of the Kv1.2 potassium channel in the resting state and by exploring the distance histograms between spin-labels attached to T4 lysozyme. The resulting VSD structures are in good agreement with
Modeling and Bio molecular Self-assembly via Molecular Dynamics and Dissipative Particle Dynamics
NASA Astrophysics Data System (ADS)
Rakesh, L.
2009-09-01
Surfactants like materials can be used to increase the solubility of poorly soluble drugs in water and to increase drug bioavailability. A typical case study will be demonstrated using DPD simulation to model the distribution of anti-inflammatory drug molecules. Computer simulation is a convenient approach to understand drug distribution and solubility concepts without much wastage and costly experiments in the laboratory. Often in molecular dynamics (MD) the atoms are represented explicitly and the equation of motion as described by Newtonian dynamics is integrated explicitly. MD has been used to study spontaneous formation of micelles by hydrophobic molecules with amphiphilic head groups in bulk water, as well as stability of pre-configured micelles and membranes. DPD is a state-of the- art mesoscale simulation, it is a more recent molecular dynamics technique, originally developed for simulating complex fluids but lately also applied to membrane dynamics, hemodynamic in biomedical applications. Such fluids pervade industrial research from paints to pharmaceuticals and from cosmetics to the controlled release of drugs. Dissipative particle dynamics (DPD) can provide structural and dynamic properties of fluids in equilibrium, under shear or confined to narrow cavities, at length- and time-scales beyond the scope of traditional atomistic molecular dynamics simulation methods. Mesoscopic particles are used to represent clusters of molecules. The interaction conserves mass and momentum and as a consequence the dynamics is consistent with Navier-Stokes equations. In addition to the conservative forces, stochastic drive and dissipation is introduced to represent internal degrees of freedom in the mesoscopic particles. In this research, an initial study is being conducted using the aqueous solubilization of the nonsteroidal, anti-inflammatory drug is studied theoretically in micellar solution of nonionic (dodecyl hexa(ethylene oxide), C12E6) surfactants possessing the
NASA Astrophysics Data System (ADS)
Powell, Jacob; Heider, Emily C.; Campiglia, Andres; Harper, James K.
2016-10-01
The ability of density functional theory (DFT) methods to predict accurate fluorescence spectra for polycyclic aromatic hydrocarbons (PAHs) is explored. Two methods, PBE0 and CAM-B3LYP, are evaluated both in the gas phase and in solution. Spectra for several of the most toxic PAHs are predicted and compared to experiment, including three isomers of C24H14 and a PAH containing heteroatoms. Unusually high-resolution experimental spectra are obtained for comparison by analyzing each PAH at 4.2 K in an n-alkane matrix. All theoretical spectra visually conform to the profiles of the experimental data but are systematically offset by a small amount. Specifically, when solvent is included the PBE0 functional overestimates peaks by 16.1 ± 6.6 nm while CAM-B3LYP underestimates the same transitions by 14.5 ± 7.6 nm. These calculated spectra can be empirically corrected to decrease the uncertainties to 6.5 ± 5.1 and 5.7 ± 5.1 nm for the PBE0 and CAM-B3LYP methods, respectively. A comparison of computed spectra in the gas phase indicates that the inclusion of n-octane shifts peaks by +11 nm on average and this change is roughly equivalent for PBE0 and CAM-B3LYP. An automated approach for comparing spectra is also described that minimizes residuals between a given theoretical spectrum and all available experimental spectra. This approach identifies the correct spectrum in all cases and excludes approximately 80% of the incorrect spectra, demonstrating that an automated search of theoretical libraries of spectra may eventually become feasible.
Thermal transpiration: A molecular dynamics study
NASA Astrophysics Data System (ADS)
T, Joe Francis; Sathian, Sarith P.
2014-12-01
Thermal transpiration is a phenomenon where fluid molecules move from the cold end towards the hot end of a channel under the influence of longitudinal temperature gradient alone. Although the phenomenon of thermal transpiration is observed at rarefied gas conditions in macro systems, the phenomenon can occur at atmospheric pressure if the characteristic dimensions of the channel is less than 100 nm. The flow through these nanosized channels is characterized by the free molecular flow regimes and continuum theory is inadequate to describe the flow. Thus a non-continuum method like molecular dynamics (MD) is necessary to study such phenomenon. In the present work, MD simulations were carried out to investigate the occurance of thermal transpiration in copper and platinum nanochannels at atmospheric pressure conditions. The mean pressure of argon gas confined inside the nano channels was maintained around 1 bar. The channel height is maintained at 2nm. The argon atoms interact with each other and with the wall atoms through the Lennard-Jones potential. The wall atoms are modelled using an EAM potential. Further, separate simulations were carried out where a Harmonic potential is used for the atom-atom interaction in the platinum channel. A thermally insulating wall was introduced between the low and high temperature regions and those wall atoms interact with fluid atoms through a repulsive potential. A reduced cut off radius were used to achieve this. Thermal creep is induced by applying a temperature gradient along the channel wall. It was found that flow developed in the direction of the increasing temperature gradient of the wall. An increase in the volumetric flux was observed as the length of the cold and the hot regions of the wall were increased. The effect of temperature gradient and the wall-fluid interaction strength on the flow parameters have been studied to understand the phenomenon better.
Thermal transpiration: A molecular dynamics study
T, Joe Francis; Sathian, Sarith P.
2014-12-09
Thermal transpiration is a phenomenon where fluid molecules move from the cold end towards the hot end of a channel under the influence of longitudinal temperature gradient alone. Although the phenomenon of thermal transpiration is observed at rarefied gas conditions in macro systems, the phenomenon can occur at atmospheric pressure if the characteristic dimensions of the channel is less than 100 nm. The flow through these nanosized channels is characterized by the free molecular flow regimes and continuum theory is inadequate to describe the flow. Thus a non-continuum method like molecular dynamics (MD) is necessary to study such phenomenon. In the present work, MD simulations were carried out to investigate the occurance of thermal transpiration in copper and platinum nanochannels at atmospheric pressure conditions. The mean pressure of argon gas confined inside the nano channels was maintained around 1 bar. The channel height is maintained at 2nm. The argon atoms interact with each other and with the wall atoms through the Lennard-Jones potential. The wall atoms are modelled using an EAM potential. Further, separate simulations were carried out where a Harmonic potential is used for the atom-atom interaction in the platinum channel. A thermally insulating wall was introduced between the low and high temperature regions and those wall atoms interact with fluid atoms through a repulsive potential. A reduced cut off radius were used to achieve this. Thermal creep is induced by applying a temperature gradient along the channel wall. It was found that flow developed in the direction of the increasing temperature gradient of the wall. An increase in the volumetric flux was observed as the length of the cold and the hot regions of the wall were increased. The effect of temperature gradient and the wall-fluid interaction strength on the flow parameters have been studied to understand the phenomenon better.
Prasad, Manish; Sinno, Talid
2004-11-01
An efficient approach is presented for performing efficient molecular dynamics simulations of solute aggregation in crystalline solids. The method dynamically divides the total simulation space into "active" regions centered about each minority species, in which regular molecular dynamics is performed. The number, size, and shape of these regions is updated periodically based on the distribution of solute atoms within the overall simulation cell. The remainder of the system is essentially static except for periodic rescaling of the entire simulation cell in order to balance the pressure between the isolated molecular dynamics regions. The method is shown to be accurate and robust for the Environment-Dependant Interatomic Potential (EDIP) for silicon and an Embedded Atom Method potential (EAM) for copper. Several tests are performed beginning with the diffusion of a single vacancy all the way to large-scale simulations of vacancy clustering. In both material systems, the predicted evolutions agree closely with the results of standard molecular dynamics simulations. Computationally, the method is demonstrated to scale almost linearly with the concentration of solute atoms, but is essentially independent of the total system size. This scaling behavior allows for the full dynamical simulation of aggregation under conditions that are more experimentally realizable than would be possible with standard molecular dynamics.
Nanoscale deicing by molecular dynamics simulation
NASA Astrophysics Data System (ADS)
Xiao, Senbo; He, Jianying; Zhang, Zhiliang
2016-07-01
Deicing is important to human activities in low-temperature circumstances, and is critical for combating the damage caused by excessive accumulation of ice. The aim of creating anti-icing materials, surfaces and applications relies on the understanding of fundamental nanoscale ice adhesion mechanics. Here in this study, we employ all-atom modeling and molecular dynamics simulation to investigate ice adhesion. We apply force to detach and shear nano-sized ice cubes for probing the determinants of atomistic adhesion mechanics, and at the same time investigate the mechanical effect of a sandwiched aqueous water layer between ice and substrates. We observe that high interfacial energy restricts ice mobility and increases both ice detaching and shearing stresses. We quantify up to a 60% decrease in ice adhesion strength by an aqueous water layer, and provide atomistic details that support previous experimental studies. Our results contribute quantitative comparison of nanoscale adhesion strength of ice on hydrophobic and hydrophilic surfaces, and supply for the first time theoretical references for understanding the mechanics at the atomistic origins of macroscale ice adhesion.Deicing is important to human activities in low-temperature circumstances, and is critical for combating the damage caused by excessive accumulation of ice. The aim of creating anti-icing materials, surfaces and applications relies on the understanding of fundamental nanoscale ice adhesion mechanics. Here in this study, we employ all-atom modeling and molecular dynamics simulation to investigate ice adhesion. We apply force to detach and shear nano-sized ice cubes for probing the determinants of atomistic adhesion mechanics, and at the same time investigate the mechanical effect of a sandwiched aqueous water layer between ice and substrates. We observe that high interfacial energy restricts ice mobility and increases both ice detaching and shearing stresses. We quantify up to a 60% decrease in ice
How Dynamic Visualization Technology Can Support Molecular Reasoning
ERIC Educational Resources Information Center
Levy, Dalit
2013-01-01
This paper reports the results of a study aimed at exploring the advantages of dynamic visualization for the development of better understanding of molecular processes. We designed a technology-enhanced curriculum module in which high school chemistry students conduct virtual experiments with dynamic molecular visualizations of solid, liquid, and…
Are current molecular dynamics force fields too helical?
Best, Robert B; Buchete, Nicolae-Viorel; Hummer, Gerhard
2008-07-01
Accurate force fields are essential for the success of molecular dynamics simulations. In apparent contrast to the conformational preferences of most force fields, recent NMR experiments suggest that short polyalanine peptides in water populate the polyproline II structure almost exclusively. To investigate this apparent contradiction, with its ramifications for the assessment of molecular force fields and the structure of unfolded proteins, we performed extensive simulations of Ala(5) in water ( approximately 5 micros total time), using twelve different force fields and three different peptide terminal groups. Using either empirical or density-functional-based Karplus relations for the J-couplings, we find that most current force fields do overpopulate the alpha-region, with quantitative results depending on the choice of Karplus relation and on the peptide termini. Even after reweighting to match experiment, we find that Ala(5) retains significant alpha- and beta-populations. In fact, several force fields match the experimental data well before reweighting and have a significant helical population. We conclude that radical changes to the best current force fields are not necessary, based on the NMR data. Nevertheless, experiments on short peptides open the way toward the systematic improvement of current simulation models.
Celeste, Ricardo; Maringolo, Milena P; Comar, Moacyr; Viana, Rommel B; Guimarães, Amanda R; Haiduke, Roberto L A; da Silva, Albérico B F
2015-10-01
Accurate Gaussian basis sets for atoms from H to Ba were obtained by means of the generator coordinate Hartree-Fock (GCHF) method based on a polynomial expansion to discretize the Griffin-Wheeler-Hartree-Fock equations (GWHF). The discretization of the GWHF equations in this procedure is based on a mesh of points not equally distributed in contrast with the original GCHF method. The results of atomic Hartree-Fock energies demonstrate the capability of these polynomial expansions in designing compact and accurate basis sets to be used in molecular calculations and the maximum error found when compared to numerical values is only 0.788 mHartree for indium. Some test calculations with the B3LYP exchange-correlation functional for N2, F2, CO, NO, HF, and HCN show that total energies within 1.0 to 2.4 mHartree compared to the cc-pV5Z basis sets are attained with our contracted bases with a much smaller number of polarization functions (2p1d and 2d1f for hydrogen and heavier atoms, respectively). Other molecular calculations performed here are also in very good accordance with experimental and cc-pV5Z results. The most important point to be mentioned here is that our generator coordinate basis sets required only a tiny fraction of the computational time when compared to B3LYP/cc-pV5Z calculations.
Rempi Studies of Molecular Reaction Dynamics.
NASA Astrophysics Data System (ADS)
Black, John Forbes
Available from UMI in association with The British Library. Requires signed TDF. Resonance-Enhanced Multi-Photon Ionisation (REMPI qv.) is used to prepare and probe systems undergoing unimolecular decomposition. It is shown that the highly efficient state selective nature of the REMPI process is well suited to both highly dynamical situations such as the "A-Band" dissociation of MeI at around 280nm and to the slower "Quasi-statistical" dissociations of the mainifold of states of the MeI(+) cation. In the study of the neutral dissociation we attempt to extract the population distributions of the quantum states "by implication" as has been done previously. We demonstrate the failings of the time-of-flight technique in being unable to do this effectively. A comparison with previous studies is made. We report the first rotationally resolved spectrum of a polyatomic (N atoms > 2) photofragment (Me from the "A-Band" photodissociation of MeI) and propose a mechanism to account for the observed differences of the rotational populations in the different dissociation channels. Two-photon linestrength theory incorporating alignment effects is extended to symmetric tops to analyse the data. The pre-dissociation dynamics of a high lying Rydberg state of the methyl radical have been extracted as part of a spectroscopic study performed on CH _3 and CD_3. The dynamics are compared to existing studies on the near-neighbours NH_3 and ND_3 with some apparent correlation. In the dissociations of the A and B states of the MeI(+) cation we are able to provide some more evidence for existing ideas that the A state dissociates by rapid inter-conversion to highly excited levels of the ground state whereas the B state dissociates in a more direct manner. We identify two existing features in the REMPI spectrum of MeI in the "A-Band" region as molecular Rydberg resonances and show that an interesting competition exists between the direct photodissociation and the "virtual" state involved in
Molecular dynamics simulations of unsaturated lipid bilayers
NASA Astrophysics Data System (ADS)
Rabinovich, Alexander L.; Balabaev, Nikolay K.
2001-02-01
Molecular dynamics simulations were carried out for bilayers of lipid molecules having stearic acid (C18:0) chain in position '3-D' (using the nomenclature of M. Sundaralingam, 1972) and fatty acid chain C18:0, C18:1(omega 9), C18:2(omega 6), C18:3(omega 3), C20:4(omega 6) or C22:6(omega 3) in position '2-D'. To investigate the properties of the bilayers two models were considered. In the first model, the simulation cells of the bilayers consisted of 96 phosphatidylcholine (PC) molecules and 2304 water molecules: 48 lipid molecules per layer and 24 H2O molecules per lipid. The water was modeled by explicit TIP3P water molecules. In the second model, the head group of the lipid molecules was treated as an effective sphere -- diacylglycerolipids (DGs) were considered, the interface of each monolayer was modeled by a flat surface; no water molecules were present explicitly. The bilayers consisted of 48 X 2 equals 96 glycerolipids arranged in a rectangular simulation cell. Various properties of the bilayers -- the C-H bond order parameter -SCH profiles of the hydrocarbon tails, the root-mean-square values of the positional fluctuations of the lipid chain carbons, mass density distributions of lipid molecules and water along the normals were investigated.
Molecular dynamics simulations of unsaturated lipid bilayers
NASA Astrophysics Data System (ADS)
Rabinovich, Alexander L.; Balabaev, Nikolay K.
2000-02-01
Molecular dynamics simulations were carried out for bilayers of lipid molecules having stearic acid (C18:0) chain in position '3-D' (using the nomenclature of M. Sundaralingam, 1972) and fatty acid chain C18:0, C18:1(omega 9), C18:2(omega 6), C18:3(omega 3), C20:4(omega 6) or C22:6(omega 3) in position '2-D'. To investigate the properties of the bilayers two models were considered. In the first model, the simulation cells of the bilayers consisted of 96 phosphatidylcholine (PC) molecules and 2304 water molecules: 48 lipid molecules per layer and 24 H2O molecules per lipid. The water was modeled by explicit TIP3P water molecules. In the second model, the head group of the lipid molecules was treated as an effective sphere -- diacylglycerolipids (DGs) were considered, the interface of each monolayer was modeled by a flat surface; no water molecules were present explicitly. The bilayers consisted of 48 X 2 equals 96 glycerolipids arranged in a rectangular simulation cell. Various properties of the bilayers -- the C-H bond order parameter -SCH profiles of the hydrocarbon tails, the root-mean-square values of the positional fluctuations of the lipid chain carbons, mass density distributions of lipid molecules and water along the normals were investigated.
Molecular chaperone-mediated nuclear protein dynamics.
Echtenkamp, Frank J; Freeman, Brian C
2014-05-01
Homeostasis requires effective action of numerous biological pathways including those working along a genome. The variety of processes functioning in the nucleus is considerable, yet the number of employed factors eclipses this total. Ideally, individual components assemble into distinct complexes and serially operate along a pathway to perform work. Adding to the complexity is a multitude of fluctuating internal and external signals that must be monitored to initiate, continue or halt individual activities. While cooperative interactions between proteins of the same process provide a mechanism for rapid and precise assembly, the inherent stability of such organized structures interferes with the proper timing of biological events. Further prolonging the longevity of biological complexes are crowding effects resulting from the high concentration of intracellular macromolecules. Hence, accessory proteins are required to destabilize the various assemblies to efficiently transition between structures, avoid off-pathway competitive interactions, and to terminate pathway activity. We suggest that molecular chaperones have evolved, in part, to manage these challenges by fostering a general and continuous dynamic protein environment within the nucleus. PMID:24694369
Molecular chaperone-mediated nuclear protein dynamics.
Echtenkamp, Frank J; Freeman, Brian C
2014-05-01
Homeostasis requires effective action of numerous biological pathways including those working along a genome. The variety of processes functioning in the nucleus is considerable, yet the number of employed factors eclipses this total. Ideally, individual components assemble into distinct complexes and serially operate along a pathway to perform work. Adding to the complexity is a multitude of fluctuating internal and external signals that must be monitored to initiate, continue or halt individual activities. While cooperative interactions between proteins of the same process provide a mechanism for rapid and precise assembly, the inherent stability of such organized structures interferes with the proper timing of biological events. Further prolonging the longevity of biological complexes are crowding effects resulting from the high concentration of intracellular macromolecules. Hence, accessory proteins are required to destabilize the various assemblies to efficiently transition between structures, avoid off-pathway competitive interactions, and to terminate pathway activity. We suggest that molecular chaperones have evolved, in part, to manage these challenges by fostering a general and continuous dynamic protein environment within the nucleus.
Nanoscale deicing by molecular dynamics simulation.
Xiao, Senbo; He, Jianying; Zhang, Zhiliang
2016-08-14
Deicing is important to human activities in low-temperature circumstances, and is critical for combating the damage caused by excessive accumulation of ice. The aim of creating anti-icing materials, surfaces and applications relies on the understanding of fundamental nanoscale ice adhesion mechanics. Here in this study, we employ all-atom modeling and molecular dynamics simulation to investigate ice adhesion. We apply force to detach and shear nano-sized ice cubes for probing the determinants of atomistic adhesion mechanics, and at the same time investigate the mechanical effect of a sandwiched aqueous water layer between ice and substrates. We observe that high interfacial energy restricts ice mobility and increases both ice detaching and shearing stresses. We quantify up to a 60% decrease in ice adhesion strength by an aqueous water layer, and provide atomistic details that support previous experimental studies. Our results contribute quantitative comparison of nanoscale adhesion strength of ice on hydrophobic and hydrophilic surfaces, and supply for the first time theoretical references for understanding the mechanics at the atomistic origins of macroscale ice adhesion. PMID:27431975
Integrating influenza antigenic dynamics with molecular evolution
Bedford, Trevor; Suchard, Marc A; Lemey, Philippe; Dudas, Gytis; Gregory, Victoria; Hay, Alan J; McCauley, John W; Russell, Colin A; Smith, Derek J; Rambaut, Andrew
2014-01-01
Influenza viruses undergo continual antigenic evolution allowing mutant viruses to evade host immunity acquired to previous virus strains. Antigenic phenotype is often assessed through pairwise measurement of cross-reactivity between influenza strains using the hemagglutination inhibition (HI) assay. Here, we extend previous approaches to antigenic cartography, and simultaneously characterize antigenic and genetic evolution by modeling the diffusion of antigenic phenotype over a shared virus phylogeny. Using HI data from influenza lineages A/H3N2, A/H1N1, B/Victoria and B/Yamagata, we determine patterns of antigenic drift across viral lineages, showing that A/H3N2 evolves faster and in a more punctuated fashion than other influenza lineages. We also show that year-to-year antigenic drift appears to drive incidence patterns within each influenza lineage. This work makes possible substantial future advances in investigating the dynamics of influenza and other antigenically-variable pathogens by providing a model that intimately combines molecular and antigenic evolution. DOI: http://dx.doi.org/10.7554/eLife.01914.001 PMID:24497547
Molecular Dynamics Simulations of Coulomb Explosion
Bringa, E M
2002-05-17
A swift ion creates a track of electronic excitations in the target material. A net repulsion inside the track can cause a ''Coulomb Explosion'', which can lead to damage and sputtering of the material. Here we report results from molecular-dynamics (MD) simulations of Coulomb explosion for a cylindrical track as a function of charge density and neutralization/quenching time, {tau}. Screening by the free electrons is accounted for using a screened Coulomb potential for the interaction among charges. The yield exhibits a prompt component from the track core and a component, which dominates at higher excitation density, from the heated region produced. For the cases studied, the number of atoms ejected per incident ion, i.e. the sputtering yield Y, is quadratic with charge density along the track as suggested by simple models. Y({tau} = 0.2 Debye periods) is nearly 20% of the yield when there is no neutralization ({tau} {yields} {infinity}). The connections between ''Coulomb explosions'', thermal spikes and measurements of electronic sputtering are discussed.
Fracture simulations via massively parallel molecular dynamics
Holian, B.L.; Abraham, F.F.; Ravelo, R.
1993-09-01
Fracture simulations at the atomistic level have heretofore been carried out for relatively small systems of particles, typically 10,000 or less. In order to study anything approaching a macroscopic system, massively parallel molecular dynamics (MD) must be employed. In two spatial dimensions (2D), it is feasible to simulate a sample that is 0.1 {mu}m on a side. We report on recent MD simulations of mode I crack extension under tensile loading at high strain rates. The method of uniaxial, homogeneously expanding periodic boundary conditions was employed to represent tensile stress conditions near the crack tip. The effects of strain rate, temperature, material properties (equation of state and defect energies), and system size were examined. We found that, in order to mimic a bulk sample, several tricks (in addition to expansion boundary conditions) need to be employed: (1) the sample must be pre-strained to nearly the condition at which the crack will spontaneously open; (2) to relieve the stresses at free surfaces, such as the initial notch, annealing by kinetic-energy quenching must be carried out to prevent unwanted rarefactions; (3) sound waves emitted as the crack tip opens and dislocations emitted from the crack tip during blunting must be absorbed by special reservoir regions. The tricks described briefly in this paper will be especially important to carrying out feasible massively parallel 3D simulations via MD.
Molecular dynamics simulations of gold nanomaterials
NASA Astrophysics Data System (ADS)
Wang, Yanting
We have carried out Molecular Dynamics simulations to study the thermal stability and melting behavior of gold nanoclusters and gold nanorods. The surface is found to play a very important role in both gold nanomaterials. Upon cooling from the liquid, we find that gold nanoclusters with 600-3000 atoms crystallize into a Mackay icosahedron. Upon heating, the {111} facets on the surface of the Mackay icosahedral gold nanoclusters soften but do not premelt below the bulk melting temperature. We attribute this surface softening to the increasing mobility of vertex and edge atoms with temperature, which leads to inter-layer and intra-layer diffusion, and a shrinkage of the average facet size. Upon heating, our simulated gold nanorods undergo a shape transformation preceding the melting transition. The shape transformation is induced by a minimization of the surface free energy, and is accompanied by a complete reconstruction of the internal structure driven by the surface change. During the transformation, the atoms on the end caps of the rod move to the sides of the rods, leading the rods to be shorter and wider. After the transformation, the surface of the stable intermediate state rod is mostly covered by the more stable {111} facets, other than the less stable {110} and {100} facets covering the sides of the initial constructed rod.
Molecular dynamics studies of lanthanum chloride solutions
Meier, W.; Bopp, Ph. ); Probst, M.M. ); Spohr, E. ); Lin, J.L. )
1990-05-31
Molecular dynamics studies are reported for LaCl{sub 3} solutions at two different concentrations and temperatures, and for isolated aqueous La{sup 3+} ions. Ion-water clusters La(H{sub 2}O){sub n}{sup 3+} with n = 61 and n = 100 and systems consisting of one ion and 100 or 200 water molecules in the usual periodic box, as well as solutions of 7 (4) cations and 21 (12) anions in 190 (200) water molecules, corresponding to 2 and 1.1 m solutions, respectively, were investigated. The 2 m solution was investigated at two different temperatures. The results for the static structure, with special emphasis on the hydration structure of the La{sup 3+} ion, are discussed in terms of radial distribution functions and resulting hydration numbers, and various other correlations. These results are compared with X-ray data and discussed in light of the hydration numbers observed for aqueous ions in general.
Efficient compression of molecular dynamics trajectory files.
Marais, Patrick; Kenwood, Julian; Smith, Keegan Carruthers; Kuttel, Michelle M; Gain, James
2012-10-15
We investigate whether specific properties of molecular dynamics trajectory files can be exploited to achieve effective file compression. We explore two classes of lossy, quantized compression scheme: "interframe" predictors, which exploit temporal coherence between successive frames in a simulation, and more complex "intraframe" schemes, which compress each frame independently. Our interframe predictors are fast, memory-efficient and well suited to on-the-fly compression of massive simulation data sets, and significantly outperform the benchmark BZip2 application. Our schemes are configurable: atomic positional accuracy can be sacrificed to achieve greater compression. For high fidelity compression, our linear interframe predictor gives the best results at very little computational cost: at moderate levels of approximation (12-bit quantization, maximum error ≈ 10(-2) Å), we can compress a 1-2 fs trajectory file to 5-8% of its original size. For 200 fs time steps-typically used in fine grained water diffusion experiments-we can compress files to ~25% of their input size, still substantially better than BZip2. While compression performance degrades with high levels of quantization, the simulation error is typically much greater than the associated approximation error in such cases.
Quantum molecular dynamics simulations of dense matter
Collins, L.; Kress, J.; Troullier, N.; Lenosky, T.; Kwon, I.
1997-12-31
The authors have developed a quantum molecular dynamics (QMD) simulation method for investigating the properties of dense matter in a variety of environments. The technique treats a periodically-replicated reference cell containing N atoms in which the nuclei move according to the classical equations-of-motion. The interatomic forces are generated from the quantum mechanical interactions of the (between?) electrons and nuclei. To generate these forces, the authors employ several methods of varying sophistication from the tight-binding (TB) to elaborate density functional (DF) schemes. In the latter case, lengthy simulations on the order of 200 atoms are routinely performed, while for the TB, which requires no self-consistency, upwards to 1000 atoms are systematically treated. The QMD method has been applied to a variety cases: (1) fluid/plasma Hydrogen from liquid density to 20 times volume-compressed for temperatures of a thousand to a million degrees Kelvin; (2) isotopic hydrogenic mixtures, (3) liquid metals (Li, Na, K); (4) impurities such as Argon in dense hydrogen plasmas; and (5) metal/insulator transitions in rare gas systems (Ar,Kr) under high compressions. The advent of parallel versions of the methods, especially for fast eigensolvers, presage LDA simulations in the range of 500--1000 atoms and TB runs for tens of thousands of particles. This leap should allow treatment of shock chemistry as well as large-scale mixtures of species in highly transient environments.
Comparing molecular dynamics force fields in the essential subspace.
Martín-García, Fernando; Papaleo, Elena; Gomez-Puertas, Paulino; Boomsma, Wouter; Lindorff-Larsen, Kresten
2015-01-01
The continued development and utility of molecular dynamics simulations requires improvements in both the physical models used (force fields) and in our ability to sample the Boltzmann distribution of these models. Recent developments in both areas have made available multi-microsecond simulations of two proteins, ubiquitin and Protein G, using a number of different force fields. Although these force fields mostly share a common mathematical form, they differ in their parameters and in the philosophy by which these were derived, and previous analyses showed varying levels of agreement with experimental NMR data. To complement the comparison to experiments, we have performed a structural analysis of and comparison between these simulations, thereby providing insight into the relationship between force-field parameterization, the resulting ensemble of conformations and the agreement with experiments. In particular, our results show that, at a coarse level, many of the motional properties are preserved across several, though not all, force fields. At a finer level of detail, however, there are distinct differences in both the structure and dynamics of the two proteins, which can, together with comparison with experimental data, help to select force fields for simulations of proteins. A noteworthy observation is that force fields that have been reparameterized and improved to provide a more accurate energetic description of the balance between helical and coil structures are difficult to distinguish from their "unbalanced" counterparts in these simulations. This observation implies that simulations of stable, folded proteins, even those reaching 10 microseconds in length, may provide relatively little information that can be used to modify torsion parameters to achieve an accurate balance between different secondary structural elements.
Comparing molecular dynamics force fields in the essential subspace.
Martín-García, Fernando; Papaleo, Elena; Gomez-Puertas, Paulino; Boomsma, Wouter; Lindorff-Larsen, Kresten
2015-01-01
The continued development and utility of molecular dynamics simulations requires improvements in both the physical models used (force fields) and in our ability to sample the Boltzmann distribution of these models. Recent developments in both areas have made available multi-microsecond simulations of two proteins, ubiquitin and Protein G, using a number of different force fields. Although these force fields mostly share a common mathematical form, they differ in their parameters and in the philosophy by which these were derived, and previous analyses showed varying levels of agreement with experimental NMR data. To complement the comparison to experiments, we have performed a structural analysis of and comparison between these simulations, thereby providing insight into the relationship between force-field parameterization, the resulting ensemble of conformations and the agreement with experiments. In particular, our results show that, at a coarse level, many of the motional properties are preserved across several, though not all, force fields. At a finer level of detail, however, there are distinct differences in both the structure and dynamics of the two proteins, which can, together with comparison with experimental data, help to select force fields for simulations of proteins. A noteworthy observation is that force fields that have been reparameterized and improved to provide a more accurate energetic description of the balance between helical and coil structures are difficult to distinguish from their "unbalanced" counterparts in these simulations. This observation implies that simulations of stable, folded proteins, even those reaching 10 microseconds in length, may provide relatively little information that can be used to modify torsion parameters to achieve an accurate balance between different secondary structural elements. PMID:25811178
Trajectory NG: portable, compressed, general molecular dynamics trajectories.
Spångberg, Daniel; Larsson, Daniel S D; van der Spoel, David
2011-10-01
We present general algorithms for the compression of molecular dynamics trajectories. The standard ways to store MD trajectories as text or as raw binary floating point numbers result in very large files when efficient simulation programs are used on supercomputers. Our algorithms are based on the observation that differences in atomic coordinates/velocities, in either time or space, are generally smaller than the absolute values of the coordinates/velocities. Also, it is often possible to store values at a lower precision. We apply several compression schemes to compress the resulting differences further. The most efficient algorithms developed here use a block sorting algorithm in combination with Huffman coding. Depending on the frequency of storage of frames in the trajectory, either space, time, or combinations of space and time differences are usually the most efficient. We compare the efficiency of our algorithms with each other and with other algorithms present in the literature for various systems: liquid argon, water, a virus capsid solvated in 15 mM aqueous NaCl, and solid magnesium oxide. We perform tests to determine how much precision is necessary to obtain accurate structural and dynamic properties, as well as benchmark a parallelized implementation of the algorithms. We obtain compression ratios (compared to single precision floating point) of 1:3.3-1:35 depending on the frequency of storage of frames and the system studied. PMID:21267752
Constant pressure and temperature discrete-time Langevin molecular dynamics
Grønbech-Jensen, Niels; Farago, Oded
2014-11-21
We present a new and improved method for simultaneous control of temperature and pressure in molecular dynamics simulations with periodic boundary conditions. The thermostat-barostat equations are built on our previously developed stochastic thermostat, which has been shown to provide correct statistical configurational sampling for any time step that yields stable trajectories. Here, we extend the method and develop a set of discrete-time equations of motion for both particle dynamics and system volume in order to seek pressure control that is insensitive to the choice of the numerical time step. The resulting method is simple, practical, and efficient. The method is demonstrated through direct numerical simulations of two characteristic model systems—a one-dimensional particle chain for which exact statistical results can be obtained and used as benchmarks, and a three-dimensional system of Lennard-Jones interacting particles simulated in both solid and liquid phases. The results, which are compared against the method of Kolb and Dünweg [J. Chem. Phys. 111, 4453 (1999)], show that the new method behaves according to the objective, namely that acquired statistical averages and fluctuations of configurational measures are accurate and robust against the chosen time step applied to the simulation.
Molecular dynamics in cytochrome c oxidase Moessbauer spectra deconvolution
Bossis, Fabrizio; Palese, Luigi L.
2011-01-07
Research highlights: {yields} Cytochrome c oxidase molecular dynamics serve to predict Moessbauer lineshape widths. {yields} Half height widths are used in modeling of Lorentzian doublets. {yields} Such spectral deconvolutions are useful in detecting the enzyme intermediates. -- Abstract: In this work low temperature molecular dynamics simulations of cytochrome c oxidase are used to predict an experimentally observable, namely Moessbauer spectra width. Predicted lineshapes are used to model Lorentzian doublets, with which published cytochrome c oxidase Moessbauer spectra were simulated. Molecular dynamics imposed constraints to spectral lineshapes permit to obtain useful information, like the presence of multiple chemical species in the binuclear center of cytochrome c oxidase. Moreover, a benchmark of quality for molecular dynamic simulations can be obtained. Despite the overwhelming importance of dynamics in electron-proton transfer systems, limited work has been devoted to unravel how much realistic are molecular dynamics simulations results. In this work, molecular dynamics based predictions are found to be in good agreement with published experimental spectra, showing that we can confidently rely on actual simulations. Molecular dynamics based deconvolution of Moessbauer spectra will lead to a renewed interest for application of this approach in bioenergetics.
Including Quantum Effects in the Dynamics of Complex (i.e., Large)Molecular Systems
Miller, William H.
2006-04-27
The development in the 1950's and 60's of crossed molecular beam methods for studying chemical reactions at the single-collision molecular level stimulated the need and desire for theoretical methods to describe these and other dynamical processes in molecular systems. Chemical dynamics theory has made great strides in the ensuing decades, so that methods are now available for treating the quantum dynamics of small molecular systems essentially completely. For the large molecular systems that are of so much interest nowadays (e.g. chemical reactions in solution, in clusters, in nano-structures, in biological systems, etc.), however, the only generally available theoretical approach is classical molecular dynamics (MD) simulations. Much effort is currently being devoted to the development of approaches for describing the quantum dynamics of these complex systems. This paper reviews some of these approaches, especially the use of semiclassical approximations for adding quantum effects to classical MD simulations, also showing some new versions that should make these semiclassical approaches even more practical and accurate.
Pierce, Levi C. T.; Markwick, Phineus R. L.; McCammon, J. Andrew; Doltsinis, Nikos L.
2011-01-01
A biased potential molecular dynamics simulation approach, accelerated molecular dynamics (AMD), has been implemented in the framework of ab initio molecular dynamics for the study of chemical reactions. Using two examples, the double proton transfer reaction in formic acid dimer and the hypothetical adiabatic ring opening and subsequent rearrangement reactions in methylenecyclopropane, it is demonstrated that ab initio AMD can be readily employed to efficiently explore the reactive potential energy surface, allowing the prediction of chemical reactions and the identification of metastable states. An adaptive variant of the AMD method is developed, which additionally affords an accurate representation of both the free-energy surface and the mechanism associated with the chemical reaction of interest and can also provide an estimate of the reaction rate. PMID:21548673
Combined molecular dynamics-spin dynamics simulations of bcc iron
Perera, Meewanage Dilina N; Yin, Junqi; Landau, David P; Nicholson, Don M; Stocks, George Malcolm; Eisenbach, Markus; Brown, Greg
2014-01-01
Using a classical model that treats translational and spin degrees of freedom on an equal footing, we study phonon-magnon interactions in BCC iron with combined molecular and spin dynamics methods. The atomic interactions are modeled via an empirical many-body potential while spin dependent interactions are established through a Hamiltonian of the Heisenberg form with a distance dependent magnetic exchange interaction obtained from first principles electronic structure calculations. The temporal evolution of translational and spin degrees of freedom was determined by numerically solving the coupled equations of motion, using an algorithm based on the second order Suzuki-Trotter decomposition of the exponential operators. By calculating Fourier transforms of space- and time-displaced correlation functions, we demonstrate that the the presence of lattice vibrations leads to noticeable softening and damping of spin wave modes. As a result of the interplay between lattice and spin subsystems, we also observe additional longitudinal spin wave excitations, with frequencies which coincide with that of the longitudinal lattice vibrations.
Molecular dynamics of biaxial nematic liquid crystals
NASA Astrophysics Data System (ADS)
Sarman, Sten
1996-01-01
We devise a constraint algorithm that makes the angular velocity of the director of a liquid crystal a constant of motion. When the angular velocity is set equal to zero, a director based coordinate system becomes an inertial frame. This is a great advantage because most thermodynamic properties and time correlation functions of a liquid crystal are best expressed relative to a director based coordinate system. One also prevents the director reorientation from interfering with the tails of the time correlation functions. When the angular velocity is forced to be zero the constraints do not do any work on the system. This makes it possible to prove that ensemble averages of phase functions and time correlation functions are unaffected by the director constraint torques. The constraint algorithm also facilitates generalization of nonequilibrium molecular dynamics algorithms to liquid crystal phases. In order to test the algorithm numerically we have simulated a biaxial nematic phase of a variant of the Gay-Berne fluid [J. G. Gay and B. J. Berne, J. Chem. Phys. 74, 3316 (1981)]. The director constraint algorithm works very well. We have calculated the velocity autocorrelation functions and the self diffusion coefficients. In a biaxial nematic liquid crystal there are three independent components of the self-diffusion tensor. They have been found to be finite and different thus proving that we really simulate a liquid rather than a solid and that the symmetry is biaxial. Simulation of biaxial liquid crystals requires fairly large systems. We have therefore developed an algorithm that we run on a parallel computer instead of an ordinary work station.
Accurate CO{sub 2} laser frequencies and molecular constants of regular and new hot-band lines
Chou, Che-Chung; Shy, Jow-Tsong; Maki, A.G.
1994-12-31
A new, high-resolution, highly efficient, cw, CO{sub 2} laser oscillating on more than 250 lines including over 40 lines in the new 9 {mu}m hot band has been built at NIST, Boulder. The frequencies of the 9 and 10 {mu}m hot band lines and high J (to J=66) regular band lines of {sup 12}C{sup 16}O{sub 2} , which now fill the gap between the 9 and 10 {mu}m regions, have been locked to saturated fluorescence signals in CO{sub 2}, and measured. New molecular constants and more accurate frequencies of the four common isotopes of CO{sub 2} have been obtained.
NASA Astrophysics Data System (ADS)
Kluber, Alexander; Hayre, Robert; Cox, Daniel
2012-02-01
Motivated by the need to find beta-structure aggregation nuclei for the polyQ diseases such as Huntington's, we have undertaken a search for length dependent structure in model polyglutamine proteins. We use the Onufriev-Bashford-Case (OBC) generalized Born implicit solvent GPU based AMBER11 molecular dynamics with the parm96 force field coupled with a replica exchange method to characterize monomeric strands of polyglutamine as a function of chain length and temperature. This force field and solvation method has been shown among other methods to accurately reproduce folded metastability in certain small peptides, and to yield accurately de novo folded structures in a millisecond time-scale protein. Using GPU molecular dynamics we can sample out into the microsecond range. Additionally, explicit solvent runs will be used to verify results from the implicit solvent runs. We will assess order using measures of secondary structure and hydrogen bond content.
Ke, Guoliang; Wang, Chunming; Ge, Yun; Zheng, Nanfeng; Zhu, Zhi; Yang, Chaoyong James
2012-11-21
Noninvasive and accurate measurement of intracellular temperature is of great significance in biology and medicine. This paper describes a safe, stable, and accurate intracellular nano-thermometer based on an L-DNA molecular beacon (L-MB), a dual-labeled hairpin oligonucleotide built from the optical isomer of naturally occurring d-DNA. Relying on the temperature-responsive hairpin structure and the FRET signaling mechanism of MBs, the fluorescence of L-MBs is quenched below the melting temperature and enhanced with increasing temperature. Because of the excellent reversibility and tunable response range, L-MBs are very suitable for temperature sensing. More importantly, the non-natural L-DNA backbone prevents the L-MBs from binding to cellular nucleic acids and proteins as well as from being digested by nucleases inside the cells, thus ensuring excellent stability and accuracy of the nano-thermometer in a complex cellular environment. The L-MB nano-thermometer was used for the photothermal study of Pd nanosheets in living cells, establishing the nano-thermometer as a useful tool for intracellular temperature measurement.
Dunn, Nicholas J. H.; Noid, W. G.
2015-12-28
The present work investigates the capability of bottom-up coarse-graining (CG) methods for accurately modeling both structural and thermodynamic properties of all-atom (AA) models for molecular liquids. In particular, we consider 1, 2, and 3-site CG models for heptane, as well as 1 and 3-site CG models for toluene. For each model, we employ the multiscale coarse-graining method to determine interaction potentials that optimally approximate the configuration dependence of the many-body potential of mean force (PMF). We employ a previously developed “pressure-matching” variational principle to determine a volume-dependent contribution to the potential, U{sub V}(V), that approximates the volume-dependence of the PMF. We demonstrate that the resulting CG models describe AA density fluctuations with qualitative, but not quantitative, accuracy. Accordingly, we develop a self-consistent approach for further optimizing U{sub V}, such that the CG models accurately reproduce the equilibrium density, compressibility, and average pressure of the AA models, although the CG models still significantly underestimate the atomic pressure fluctuations. Additionally, by comparing this array of models that accurately describe the structure and thermodynamic pressure of heptane and toluene at a range of different resolutions, we investigate the impact of bottom-up coarse-graining upon thermodynamic properties. In particular, we demonstrate that U{sub V} accounts for the reduced cohesion in the CG models. Finally, we observe that bottom-up coarse-graining introduces subtle correlations between the resolution, the cohesive energy density, and the “simplicity” of the model.
NASA Astrophysics Data System (ADS)
Dunn, Nicholas J. H.; Noid, W. G.
2015-12-01
The present work investigates the capability of bottom-up coarse-graining (CG) methods for accurately modeling both structural and thermodynamic properties of all-atom (AA) models for molecular liquids. In particular, we consider 1, 2, and 3-site CG models for heptane, as well as 1 and 3-site CG models for toluene. For each model, we employ the multiscale coarse-graining method to determine interaction potentials that optimally approximate the configuration dependence of the many-body potential of mean force (PMF). We employ a previously developed "pressure-matching" variational principle to determine a volume-dependent contribution to the potential, UV(V), that approximates the volume-dependence of the PMF. We demonstrate that the resulting CG models describe AA density fluctuations with qualitative, but not quantitative, accuracy. Accordingly, we develop a self-consistent approach for further optimizing UV, such that the CG models accurately reproduce the equilibrium density, compressibility, and average pressure of the AA models, although the CG models still significantly underestimate the atomic pressure fluctuations. Additionally, by comparing this array of models that accurately describe the structure and thermodynamic pressure of heptane and toluene at a range of different resolutions, we investigate the impact of bottom-up coarse-graining upon thermodynamic properties. In particular, we demonstrate that UV accounts for the reduced cohesion in the CG models. Finally, we observe that bottom-up coarse-graining introduces subtle correlations between the resolution, the cohesive energy density, and the "simplicity" of the model.
Piquemal, Jean-Philip; Perera, Lalith; Cisneros, G Andrés; Ren, Pengyu; Pedersen, Lee G; Darden, Thomas A
2006-08-01
Molecular dynamics simulations were performed using a modified amoeba force field to determine hydration and dynamical properties of the divalent cations Ca2+ and Mg2+. The extension of amoeba to divalent cations required the introduction of a cation specific parametrization. To accomplish this, the Thole polarization damping model parametrization was modified based on the ab initio polarization energy computed by a constrained space orbital variation energy decomposition scheme. Excellent agreement has been found with condensed phase experimental results using parameters derived from gas phase ab initio calculations. Additionally, we have observed that the coordination of the calcium cation is influenced by the size of the periodic water box, a recurrent issue in first principles molecular dynamics studies.
Dispersion curves from short-time molecular dynamics simulation. 1. Diatomic chain results
Noid, D.W.; Broocks, B.T.; Gray, S.K.; Marple, S.L.
1988-06-16
The multiple signal classification method (MUSIC) for frequency estimation is used to compute the frequency dispersion curves of a diatomic chain from the time-dependent structure factor. In this paper, the authors demonstrate that MUSIC can accurately determine the frequencies from very short time trajectories. MUSIC is also used to show how the frequencies can vary in time, i.e., along a trajectory. The method is ideally suited for analyzing molecular dynamics simulations of large systems.
The Adaptively Biased Molecular Dynamics method revisited: New capabilities and an application
NASA Astrophysics Data System (ADS)
Moradi, Mahmoud; Babin, Volodymyr; Roland, Christopher; Sagui, Celeste
2015-09-01
The free energy is perhaps one of the most important quantity required for describing biomolecular systems at equilibrium. Unfortunately, accurate and reliable free energies are notoriously difficult to calculate. To address this issue, we previously developed the Adaptively Biased Molecular Dynamics (ABMD) method for accurate calculation of rugged free energy surfaces (FES). Here, we briefly review the workings of the ABMD method with an emphasis on recent software additions, along with a short summary of a selected ABMD application based on the B-to-Z DNA transition. The ABMD method, along with current extensions, is currently implemented in the AMBER (ver.10-14) software package.
Las Palmeras Molecular Dynamics: A flexible and modular molecular dynamics code
NASA Astrophysics Data System (ADS)
Davis, Sergio; Loyola, Claudia; González, Felipe; Peralta, Joaquín
2010-12-01
Las Palmeras Molecular Dynamics (LPMD) is a highly modular and extensible molecular dynamics (MD) code using interatomic potential functions. LPMD is able to perform equilibrium MD simulations of bulk crystalline solids, amorphous solids and liquids, as well as non-equilibrium MD (NEMD) simulations such as shock wave propagation, projectile impacts, cluster collisions, shearing, deformation under load, heat conduction, heterogeneous melting, among others, which involve unusual MD features like non-moving atoms and walls, unstoppable atoms with constant-velocity, and external forces like electric fields. LPMD is written in C++ as a compromise between efficiency and clarity of design, and its architecture is based on separate components or plug-ins, implemented as modules which are loaded on demand at runtime. The advantage of this architecture is the ability to completely link together the desired components involved in the simulation in different ways at runtime, using a user-friendly control file language which describes the simulation work-flow. As an added bonus, the plug-in API (Application Programming Interface) makes it possible to use the LPMD components to analyze data coming from other simulation packages, convert between input file formats, apply different transformations to saved MD atomic trajectories, and visualize dynamical processes either in real-time or as a post-processing step. Individual components, such as a new potential function, a new integrator, a new file format, new properties to calculate, new real-time visualizers, and even a new algorithm for handling neighbor lists can be easily coded, compiled and tested within LPMD by virtue of its object-oriented API, without the need to modify the rest of the code. LPMD includes already several pair potential functions such as Lennard-Jones, Morse, Buckingham, MCY and the harmonic potential, as well as embedded-atom model (EAM) functions such as the Sutton-Chen and Gupta potentials. Integrators to
CHARACTERIZING COUPLED CHARGE TRANSPORT WITH MULTISCALE MOLECULAR DYNAMICS
Swanson, Jessica
2011-08-31
This is the final progress report for Award DE-SC0004920, entitled 'Characterizing coupled charge transport with multi scale molecular dynamics'. The technical abstract will be provided in the uploaded report.
NASA Astrophysics Data System (ADS)
Pham, Tuan Anh; Ogitsu, Tadashi; Lau, Edmond Y.; Schwegler, Eric
2016-10-01
Establishing an accurate and predictive computational framework for the description of complex aqueous solutions is an ongoing challenge for density functional theory based first-principles molecular dynamics (FPMD) simulations. In this context, important advances have been made in recent years, including the development of sophisticated exchange-correlation functionals. On the other hand, simulations based on simple generalized gradient approximation (GGA) functionals remain an active field, particularly in the study of complex aqueous solutions due to a good balance between the accuracy, computational expense, and the applicability to a wide range of systems. Such simulations are often performed at elevated temperatures to artificially "correct" for GGA inaccuracies in the description of liquid water; however, a detailed understanding of how the choice of temperature affects the structure and dynamics of other components, such as solvated ions, is largely unknown. To address this question, we carried out a series of FPMD simulations at temperatures ranging from 300 to 460 K for liquid water and three representative aqueous solutions containing solvated Na+, K+, and Cl- ions. We show that simulations at 390-400 K with the Perdew-Burke-Ernzerhof (PBE) exchange-correlation functional yield water structure and dynamics in good agreement with experiments at ambient conditions. Simultaneously, this computational setup provides ion solvation structures and ion effects on water dynamics consistent with experiments. Our results suggest that an elevated temperature around 390-400 K with the PBE functional can be used for the description of structural and dynamical properties of liquid water and complex solutions with solvated ions at ambient conditions.
Masses, luminosities and dynamics of galactic molecular clouds
NASA Technical Reports Server (NTRS)
Solomon, P. M.; Rivolo, A. R.; Mooney, T. J.; Barrett, J. W.; Sage, L. J.
1987-01-01
Star formation in galaxies takes place in molecular clouds and the Milky Way is the only galaxy in which it is possible to resolve and study the physical properties and star formation activity of individual clouds. The masses, luminosities, dynamics, and distribution of molecular clouds, primarily giant molecular clouds in the Milky Way are described and analyzed. The observational data sets are the Massachusetts-Stony Brook CO Galactic Plane Survey and the IRAS far IR images. The molecular mass and infrared luminosities of glactic clouds are then compared with the molecular mass and infrared luminosities of external galaxies.
Dynamical analysis of highly excited molecular spectra
Kellman, M.E.
1993-12-01
The goal of this program is new methods for analysis of spectra and dynamics of highly excited vibrational states of molecules. In these systems, strong mode coupling and anharmonicity give rise to complicated classical dynamics, and make the simple normal modes analysis unsatisfactory. New methods of spectral analysis, pattern recognition, and assignment are sought using techniques of nonlinear dynamics including bifurcation theory, phase space classification, and quantization of phase space structures. The emphasis is chaotic systems and systems with many degrees of freedom.
Conformational properties of cyclooctane: a molecular dynamics simulation study
NASA Astrophysics Data System (ADS)
Bharadwaj, Rishikesh K.
Atomistic molecular dynamics simulations have been used to elucidate the conformational properties of cyclooctane in the gas and bulk liquid phases. Accurate reproduction of the gas phase structure, and of the liquid phase densities and solubility parameters have been used as prerequisites to the prediction of conformational properties. The gas phase results clearly indicate the presence of a conformational mixture consisting of the crown, boat-chair, twist-boat-chair and boat-boat conformers at all temperatures (161, 313 and 400K) studied. The fraction of the crown family of conformers was found to be relatively insensitive to temperature. However, the relative concentrations of the twist-boat-chair and boat-chair conformations was found to be highly temperature dependent with the boat-chair being favoured at low temperatures. Bulk packing was found to have a profound effect on the conformational properties in the liquid phase. At the temperatures studied(313 and 400K) the boat-chair family was predominant, with the crown and boat families being essentially absent. The twist-boatchair conformation was detected in the liquid phase at both temperatures. The pseudorotation pathway for the twist-boat-chair to boat-chair interconversion was prevalent in both gas and liquid phases establishing the conformational flexibility and the relative importance of the twist-boat-chair conformer in comparison to the crown family. The study successfully explains the separate experimental findings in both the gas and liquid phases of cyclooctane.
The Multifaceted Roles of Molecular Dynamics Simulations in Drug Discovery.
Fox, Stephen John; Li, Jianguo; Sing Tan, Yaw; Nguyen, Minh N; Pal, Arumay; Ouaray, Zohra; Yadahalli, Shilpa; Kannan, Srinivasaraghavan
2016-01-01
Discovery of new therapeutics is a very challenging, expensive and time-consuming process. With the number of approved drugs declining steadily, combined with increasing costs, a rational approach is needed to facilitate, expedite and streamline the drug discovery process. In silico methods are playing key roles in the discovery of a growing number of marketed drugs. The use of computational approaches, particularly molecular dynamics, in drug design is rapidly gaining momentum and acceptance as an essential part of the toolkit for modern drug discovery. From analysing atomistic details for explaining experimentally observed phenomena, to designing drugs with increased efficacy and specificity, the insight that such simulations can provide is generating new ideas and applications that have previously been unexplored. Here we discuss physics-based simulation methodologies and applications in drug design: from locating pockets to designing novel lead compounds, from small molecules to peptides. With developments in hardware, software and theory, the improved predictive abilities of in silico efforts are becoming an essential part of efficient, economic and accurate drug development strategies.
Efficiency in nonequilibrium molecular dynamics Monte Carlo simulations
NASA Astrophysics Data System (ADS)
Radak, Brian K.; Roux, Benoît
2016-10-01
Hybrid algorithms combining nonequilibrium molecular dynamics and Monte Carlo (neMD/MC) offer a powerful avenue for improving the sampling efficiency of computer simulations of complex systems. These neMD/MC algorithms are also increasingly finding use in applications where conventional approaches are impractical, such as constant-pH simulations with explicit solvent. However, selecting an optimal nonequilibrium protocol for maximum efficiency often represents a non-trivial challenge. This work evaluates the efficiency of a broad class of neMD/MC algorithms and protocols within the theoretical framework of linear response theory. The approximations are validated against constant pH-MD simulations and shown to provide accurate predictions of neMD/MC performance. An assessment of a large set of protocols confirms (both theoretically and empirically) that a linear work protocol gives the best neMD/MC performance. Finally, a well-defined criterion for optimizing the time parameters of the protocol is proposed and demonstrated with an adaptive algorithm that improves the performance on-the-fly with minimal cost.
When do perturbative approaches accurately capture the dynamics of complex quantum systems?
NASA Astrophysics Data System (ADS)
Fruchtman, Amir; Lambert, Neill; Gauger, Erik M.
2016-06-01
Understanding the dynamics of higher-dimensional quantum systems embedded in a complex environment remains a significant theoretical challenge. While several approaches yielding numerically converged solutions exist, these are computationally expensive and often provide only limited physical insight. Here we address the question: when do more intuitive and simpler-to-compute second-order perturbative approaches provide adequate accuracy? We develop a simple analytical criterion and verify its validity for the case of the much-studied FMO dynamics as well as the canonical spin-boson model.
When do perturbative approaches accurately capture the dynamics of complex quantum systems?
Fruchtman, Amir; Lambert, Neill; Gauger, Erik M.
2016-01-01
Understanding the dynamics of higher-dimensional quantum systems embedded in a complex environment remains a significant theoretical challenge. While several approaches yielding numerically converged solutions exist, these are computationally expensive and often provide only limited physical insight. Here we address the question: when do more intuitive and simpler-to-compute second-order perturbative approaches provide adequate accuracy? We develop a simple analytical criterion and verify its validity for the case of the much-studied FMO dynamics as well as the canonical spin-boson model. PMID:27335176
HTMD: High-Throughput Molecular Dynamics for Molecular Discovery.
Doerr, S; Harvey, M J; Noé, Frank; De Fabritiis, G
2016-04-12
Recent advances in molecular simulations have allowed scientists to investigate slower biological processes than ever before. Together with these advances came an explosion of data that has transformed a traditionally computing-bound into a data-bound problem. Here, we present HTMD, a programmable, extensible platform written in Python that aims to solve the data generation and analysis problem as well as increase reproducibility by providing a complete workspace for simulation-based discovery. So far, HTMD includes system building for CHARMM and AMBER force fields, projection methods, clustering, molecular simulation production, adaptive sampling, an Amazon cloud interface, Markov state models, and visualization. As a result, a single, short HTMD script can lead from a PDB structure to useful quantities such as relaxation time scales, equilibrium populations, metastable conformations, and kinetic rates. In this paper, we focus on the adaptive sampling and Markov state modeling features. PMID:26949976
Dynamics of nitrogen dissociation from direct molecular simulation
NASA Astrophysics Data System (ADS)
Valentini, Paolo; Schwartzentruber, Thomas E.; Bender, Jason D.; Candler, Graham V.
2016-08-01
dissociating nitrogen systems involving both atomic and molecular nitrogen. Such direct comparisons also illustrate how the DMS method is able to reveal all relevant nonequilibrium physics without the need to compute large numbers of state-transition probabilities. In this manner, DMS presents an accurate and tractable approach to construct models for direct-simulation Monte Carlo and computational fluid dynamics simulations from first principles.
Elucidation of molecular dynamics of invasive species of rice
Technology Transfer Automated Retrieval System (TEKTRAN)
Cultivated rice fields are aggressively invaded by weedy rice in the U.S. and worldwide. Weedy rice results in loss of yield and seed contamination. The molecular dynamics of the evolutionary adaptive traits of weedy rice are not fully understood. To understand the molecular basis and identify the i...
Attosecond molecular dynamics: fact or fiction?
NASA Astrophysics Data System (ADS)
Lépine, Franck; Ivanov, Misha Y.; Vrakking, Marc J. J.
2014-03-01
The emerging application of attosecond techniques to molecular systems allows the role of electronic coherence in the control of chemical reactions to be investigated. Prompt ionization of molecules by an attosecond pulse may induce charge migration across a molecular structure on attosecond to few-femtosecond timescales, thereby possibly determining the subsequent relaxation pathways that a molecule may take. We discuss how proposals for this 'charge-directed reactivity' fit within the current understanding of quantum control and review the current state of the art of attosecond molecular science. Specifically, we review the role of electronic coherence and coupling of the electronic and nuclear degrees of freedom in high-harmonic spectroscopy and in the first attosecond pump-probe experiments on molecular systems.
Molecular dynamics simulation of interfacial adhesion
Yarovsky, I.; Chaffee, A.L.
1996-12-31
Chromium salts are often used in the pretreatment stages of steel painting processes in order to improve adhesion at the metal oxide/primer interface. Although well established empirically, the chemical basis for the improved adhesion conferred by chromia is not well understood. A molecular level understanding of this behaviour should provide a foundation for the design of materials offering improved adhesion control. Molecular modelling of adhesion involves simulation and analysis of molecular behaviour at the interface between two interacting phases. The present study concerns behaviour at the boundary between the metal coated steel surface (with or without chromium pretreatment) and an organic primer based on a solid epoxide resin produced from bisphenol A and epichlorohydrin. An epoxy resin oligomer of molecular weight 3750 was used as the model for the primer.
Describing and compensating gas transport dynamics for accurate instantaneous emission measurement
NASA Astrophysics Data System (ADS)
Weilenmann, Martin; Soltic, Patrik; Ajtay, Delia
Instantaneous emission measurements on chassis dynamometers and engine test benches are becoming increasingly usual for car-makers and for environmental emission factor measurement and calculation, since much more information about the formation conditions can be extracted than from the regulated bag measurements (integral values). The common exhaust gas analysers for the "regulated pollutants" (carbon monoxide, total hydrocarbons, nitrogen oxide, carbon dioxide) allow measurement at a rate of one to ten samples per second. This gives the impression of having after-the-catalyst emission information with that chronological precision. It has been shown in recent years, however, that beside the reaction time of the analysers, the dynamics of gas transport in both the exhaust system of the car and the measurement system last significantly longer than 1 s. This paper focuses on the compensation of all these dynamics convoluting the emission signals. Most analysers show linear and time-invariant reaction dynamics. Transport dynamics can basically be split into two phenomena: a pure time delay accounting for the transport of the gas downstream and a dynamic signal deformation since the gas is mixed by turbulence along the way. This causes emission peaks to occur which are smaller in height and longer in time at the sensors than they are after the catalyst. These dynamics can be modelled using differential equations. Both mixing dynamics and time delay are constant for modelling a raw gas analyser system, since the flow in that system is constant. In the exhaust system of the car, however, the parameters depend on the exhaust volume flow. For gasoline cars, the variation in overall transport time may be more than 6 s. It is shown in this paper how all these processes can be described by invertible mathematical models with the focus on the more complex case of the car's exhaust system. Inversion means that the sharp emission signal at the catalyst out location can be
Interaction of monovalent ions with the water liquid-vapor interface - A molecular dynamics study
NASA Technical Reports Server (NTRS)
Wilson, Michael A.; Pohorille, Andrew
1991-01-01
Results of molecular dynamics calculations are presented for a series of ions at infinite dilution near the water liquid-vapor interface. The free energies of ion transfer from the bulk to the interface are discussed, as are the accompanying changes of water structure at the surface and ion mobilities as a function of their proximity to the interface. It is shown that simple dielectric models do not provide an accurate description of ions at the water surface. The results of the study should be useful in the development of better models incorporating the shape and molecular structure of the interface.
Sapsis, Themistoklis P.; Majda, Andrew J.
2013-01-01
A framework for low-order predictive statistical modeling and uncertainty quantification in turbulent dynamical systems is developed here. These reduced-order, modified quasilinear Gaussian (ROMQG) algorithms apply to turbulent dynamical systems in which there is significant linear instability or linear nonnormal dynamics in the unperturbed system and energy-conserving nonlinear interactions that transfer energy from the unstable modes to the stable modes where dissipation occurs, resulting in a statistical steady state; such turbulent dynamical systems are ubiquitous in geophysical and engineering turbulence. The ROMQG method involves constructing a low-order, nonlinear, dynamical system for the mean and covariance statistics in the reduced subspace that has the unperturbed statistics as a stable fixed point and optimally incorporates the indirect effect of non-Gaussian third-order statistics for the unperturbed system in a systematic calibration stage. This calibration procedure is achieved through information involving only the mean and covariance statistics for the unperturbed equilibrium. The performance of the ROMQG algorithm is assessed on two stringent test cases: the 40-mode Lorenz 96 model mimicking midlatitude atmospheric turbulence and two-layer baroclinic models for high-latitude ocean turbulence with over 125,000 degrees of freedom. In the Lorenz 96 model, the ROMQG algorithm with just a single mode captures the transient response to random or deterministic forcing. For the baroclinic ocean turbulence models, the inexpensive ROMQG algorithm with 252 modes, less than 0.2% of the total, captures the nonlinear response of the energy, the heat flux, and even the one-dimensional energy and heat flux spectra. PMID:23918398
Visualizing Functional Motions of Membrane Transporters with Molecular Dynamics Simulations
2013-01-01
Computational modeling and molecular simulation techniques have become an integral part of modern molecular research. Various areas of molecular sciences continue to benefit from, indeed rely on, the unparalleled spatial and temporal resolutions offered by these technologies, to provide a more complete picture of the molecular problems at hand. Because of the continuous development of more efficient algorithms harvesting ever-expanding computational resources, and the emergence of more advanced and novel theories and methodologies, the scope of computational studies has expanded significantly over the past decade, now including much larger molecular systems and far more complex molecular phenomena. Among the various computer modeling techniques, the application of molecular dynamics (MD) simulation and related techniques has particularly drawn attention in biomolecular research, because of the ability of the method to describe the dynamical nature of the molecular systems and thereby to provide a more realistic representation, which is often needed for understanding fundamental molecular properties. The method has proven to be remarkably successful in capturing molecular events and structural transitions highly relevant to the function and/or physicochemical properties of biomolecular systems. Herein, after a brief introduction to the method of MD, we use a number of membrane transport proteins studied in our laboratory as examples to showcase the scope and applicability of the method and its power in characterizing molecular motions of various magnitudes and time scales that are involved in the function of this important class of membrane proteins. PMID:23298176
Molecular dynamics simulations of pressure shocks in liquid phase nitromethane
NASA Astrophysics Data System (ADS)
McNatt, Michael David
The dynamic energy transfer processes present in liquid nitromethane (NM) under pressure shock loading conditions have been investigated by nonequilibrium molecular dynamics methods using a previously developed, fully flexible NM force field (Sorescu, D. C.; Rice, B. M.; Thompson, D. L. J. Phys. Chem. B 2000, 104, 8406). Generally good qualitative agreement with the corresponding experimental values was found for sound speeds (C) as a function of temperature. This is true as well for the PVT Hugoniot data calculated for the shock compressed zones behind our simulated shock fronts. The predicted C( T) are, however, ˜13--30% higher than experiment (Lysne, P. C.; Hardesty, D. R. J. Chem. Phys. 1973, 59, 6512) and our predicted densities for the shock compressed area behind fronts are consistently 4--10% lower than experiment (Winey, J. M.; Duvall, G. E.; Knudson, M. D.; Gupta, Y. M. J. Chem. Phys. 2000, 113, 7492). Accurate Hugoniot pressures are predicted by our simulations at all three initial temperatures (T i) studied. The Ti simulated for this work (255, 300, 350 K) span virtually the entire experimental ambient pressure liquid temperature range of NM (˜ 244--373 K). Thus combining and comparing our results with those of Winey et al. based on empirical equations of state work, opens up a considerable range of possible further tests and developments of our NM force field. This is particularly important in regards to the intermolecular force field due to its intended purpose of being applicable to a wide range of nitro and nitramine energetic compounds. Also, within the timeframes of our simulations (< 10 ps) the kinetic energy behind our shock fronts does not achieve equilibrium conditions as determined by the classical theory of equipartition.
Tunable Interfacial Thermal Conductance by Molecular Dynamics
NASA Astrophysics Data System (ADS)
Shen, Meng
We study the mechanism of tunable heat transfer through interfaces between solids using a combination of non-equilibrium molecular dynamics simulation (NEMD), vibrational mode analysis and wave packet simulation. We investigate how heat transfer through interfaces is affected by factors including pressure, interfacial modulus, contact area and interfacial layer thickness, with an overreaching goal of developing fundamental knowledge that will allow one to tailor thermal properties of interfacial materials. The role of pressure and interfacial stiffness is unraveled by our studies on an epitaxial interface between two Lennard-Jones (LJ) crystals. The interfacial stiffness is varied by two different methods: (i) indirectly by applying pressure which due to anharmonic nature of bonding, increases interfacial stiffness, and (ii) directly by changing the interfacial bonding strength by varying the depth of the potential well of the LJ potential. When the interfacial bonding strength is low, quantitatively similar behavior to pressure tuning is observed when the interfacial thermal conductance is increased by directly varying the potential-well depth parameter of the LJ potential. By contrast, when the interfacial bonding strength is high, thermal conductance is almost pressure independent, and even slightly decreases with increasing pressure. This decrease can be explained by the change in overlap between the vibrational densities of states of the two crystalline materials. The role of contact area is studied by modeling structures comprised of Van der Waals junctions between single-walled nanotubes (SWCNT). Interfacial thermal conductance between SWCNTs is obtained from NEMD simulation as a function of crossing angle. In this case the junction conductance per unit area is essentially a constant. By contrast, interfacial thermal conductance between multiwalled carbon nanotubes (MWCNTs) is shown to increase with diameter of the nanotubes by recent experimental studies [1
Tunable Interfacial Thermal Conductance by Molecular Dynamics
NASA Astrophysics Data System (ADS)
Shen, Meng
We study the mechanism of tunable heat transfer through interfaces between solids using a combination of non-equilibrium molecular dynamics simulation (NEMD), vibrational mode analysis and wave packet simulation. We investigate how heat transfer through interfaces is affected by factors including pressure, interfacial modulus, contact area and interfacial layer thickness, with an overreaching goal of developing fundamental knowledge that will allow one to tailor thermal properties of interfacial materials. The role of pressure and interfacial stiffness is unraveled by our studies on an epitaxial interface between two Lennard-Jones (LJ) crystals. The interfacial stiffness is varied by two different methods: (i) indirectly by applying pressure which due to anharmonic nature of bonding, increases interfacial stiffness, and (ii) directly by changing the interfacial bonding strength by varying the depth of the potential well of the LJ potential. When the interfacial bonding strength is low, quantitatively similar behavior to pressure tuning is observed when the interfacial thermal conductance is increased by directly varying the potential-well depth parameter of the LJ potential. By contrast, when the interfacial bonding strength is high, thermal conductance is almost pressure independent, and even slightly decreases with increasing pressure. This decrease can be explained by the change in overlap between the vibrational densities of states of the two crystalline materials. The role of contact area is studied by modeling structures comprised of Van der Waals junctions between single-walled nanotubes (SWCNT). Interfacial thermal conductance between SWCNTs is obtained from NEMD simulation as a function of crossing angle. In this case the junction conductance per unit area is essentially a constant. By contrast, interfacial thermal conductance between multiwalled carbon nanotubes (MWCNTs) is shown to increase with diameter of the nanotubes by recent experimental studies [1
Berger, Perrine; Alouini, Mehdi; Bourderionnet, Jérôme; Bretenaker, Fabien; Dolfi, Daniel
2010-01-18
We developed an improved model in order to predict the RF behavior and the slow light properties of the SOA valid for any experimental conditions. It takes into account the dynamic saturation of the SOA, which can be fully characterized by a simple measurement, and only relies on material fitting parameters, independent of the optical intensity and the injected current. The present model is validated by showing a good agreement with experiments for small and large modulation indices.
The Computer Simulation of Liquids by Molecular Dynamics.
ERIC Educational Resources Information Center
Smith, W.
1987-01-01
Proposes a mathematical computer model for the behavior of liquids using the classical dynamic principles of Sir Isaac Newton and the molecular dynamics method invented by other scientists. Concludes that other applications will be successful using supercomputers to go beyond simple Newtonian physics. (CW)
Temperature dependence of protein hydration hydrodynamics by molecular dynamics simulations.
Lau, E Y; Krishnan, V V
2007-07-18
The dynamics of water molecules near the protein surface are different from those of bulk water and influence the structure and dynamics of the protein itself. To elucidate the temperature dependence hydration dynamics of water molecules, we present results from the molecular dynamic simulation of the water molecules surrounding two proteins (Carboxypeptidase inhibitor and Ovomucoid) at seven different temperatures (T=273 to 303 K, in increments of 5 K). Translational diffusion coefficients of the surface water and bulk water molecules were estimated from 2 ns molecular dynamics simulation trajectories. Temperature dependence of the estimated bulk water diffusion closely reflects the experimental values, while hydration water diffusion is retarded significantly due to the protein. Protein surface induced scaling of translational dynamics of the hydration waters is uniform over the temperature range studied, suggesting the importance protein-water interactions.
NASA Astrophysics Data System (ADS)
Hardy, David J.; Wolff, Matthew A.; Xia, Jianlin; Schulten, Klaus; Skeel, Robert D.
2016-03-01
The multilevel summation method for calculating electrostatic interactions in molecular dynamics simulations constructs an approximation to a pairwise interaction kernel and its gradient, which can be evaluated at a cost that scales linearly with the number of atoms. The method smoothly splits the kernel into a sum of partial kernels of increasing range and decreasing variability with the longer-range parts interpolated from grids of increasing coarseness. Multilevel summation is especially appropriate in the context of dynamics and minimization, because it can produce continuous gradients. This article explores the use of B-splines to increase the accuracy of the multilevel summation method (for nonperiodic boundaries) without incurring additional computation other than a preprocessing step (whose cost also scales linearly). To obtain accurate results efficiently involves technical difficulties, which are overcome by a novel preprocessing algorithm. Numerical experiments demonstrate that the resulting method offers substantial improvements in accuracy and that its performance is competitive with an implementation of the fast multipole method in general and markedly better for Hamiltonian formulations of molecular dynamics. The improvement is great enough to establish multilevel summation as a serious contender for calculating pairwise interactions in molecular dynamics simulations. In particular, the method appears to be uniquely capable for molecular dynamics in two situations, nonperiodic boundary conditions and massively parallel computation, where the fast Fourier transform employed in the particle-mesh Ewald method falls short.
NASA Astrophysics Data System (ADS)
Pavese, Marc; Berard, Daniel R.; Voth, Gregory A.
1999-01-01
A fully quantum molecular dynamics method is presented which combines ab initio Car-Parrinello molecular dynamics with centroid molecular dynamics. The first technique allows the forces on the atoms to be obtained from ab initio electronic structure. The second technique, given the forces on the atoms, allows one to calculate an approximate quantum time evolution for the nuclei. The combination of the two, therefore, represents the first feasible approach to simulating the fully quantum dynamics of a many-body system. An application to excess proton translocation along a model water wire will be presented.
Molecular Dynamics in Self-Assembled Monolayers
NASA Astrophysics Data System (ADS)
Bochinski, Jason; Stevens, Derrick; Scott, Mary; Guy, Laura; Dedeugd, Casey; Clarke, Laura
2007-03-01
Silane self-assembled monolayers (SAMs) are an important tool for both scientific research and technological applications. Despite their widespread use, few experimental investigations have addressed molecular motion within these films, which offer a unique and useful physical system for fundamental scientific studies, such as observing dipolar and other glass transitions in two-dimensions. In addition, relaxations such as ``rotator'' phases where molecular groups rotate in a plane parallel to the surface have been correlated with film conductivity, adhesive, and wetting properties. We utilize surface-sensitive, dielectric relaxation spectroscopy to probe molecular motion as a function of temperature within silane chemistry-based monolayers formed upon interdigitated electrodes. Our latest results exploring a previously published motion as well as comparisons to linear polymer films will be discussed.
On electronic representations in molecular reaction dynamics
NASA Astrophysics Data System (ADS)
Killian, Benjamin J.
For many decades, the field of chemical reaction dynamics has utilized computational methods that rely on potential energy surfaces that are constructed using stationary-state calculations. These methods are typically devoid of dynamical couplings between the electronic and nuclear degrees of freedom, a fact that can result in incorrect descriptions of dynamical processes. Often, non-adiabatic coupling expressions are included in these methodologies. The Electron-Nuclear Dynamics (END) formalism, in contrast, circumvents these deficiencies by calculating all intermolecular forces directly at each time step in the dynamics and by explicitly maintaining all electronic-nuclear couplings. The purpose of this work is to offer two new frameworks for implementing electronic representations in dynamical calculations. Firstly, a new schema is proposed for developing atomic basis sets that are consistent with dynamical calculations. Traditionally, basis sets have been designed for use in stationary-state calculations of the structures and properties of molecules in their ground states. As a consequence of common construction techniques that utilize energy optimization methods, the unoccupied orbitals bear little resemblance to physical virtual atomic orbitals. We develop and implement a method for basis set construction that relies upon physical properties of atomic orbitals and that results in meaningful virtual orbitals. These basis sets are shown to provide a significant improvement in the accuracy of calculated dynamical properties such as charge transfer probabilities. Secondly, the theoretical framework of END is expanded to incorporate a multi-configurational representation for electrons. This formalism, named Vector Hartree-Fock, is based in the theory of vector coherent states and utilizes a complete active space electronic representation. The Vector Hartree-Fock method is fully disclosed, with derivation of the equations of motion. The expressions for the equation
Optimal control of molecular motion expressed through quantum fluid dynamics
NASA Astrophysics Data System (ADS)
Dey, Bijoy K.; Rabitz, Herschel; Askar, Attila
2000-04-01
A quantum fluid-dynamic (QFD) control formulation is presented for optimally manipulating atomic and molecular systems. In QFD the control quantum system is expressed in terms of the probability density ρ and the quantum current j. This choice of variables is motivated by the generally expected slowly varying spatial-temporal dependence of the fluid-dynamical variables. The QFD approach is illustrated for manipulation of the ground electronic state dynamics of HCl induced by an external electric field.
Single Molecule Spectroscopy Illuminating the Molecular Dynamics of Life
NASA Astrophysics Data System (ADS)
Webb, Watt W.
This chapter summarizes a series of new single-molecule spectroscopy investigations in the life sciences at Cornell University that began with our invention of Fluorescence Correlation Spectroscopy (FCS) about 1970. Our invention of FCS became my first focus on the "Molecular Dynamics of Life." It motivated my transition from research on quantum fluctuations and transport in condensed matter physics including superconductivity and in the molecular dynamics of coherent fluctuations and nano-transport in inanimate physical and chemical systems subject to the nonlinear dynamics of continuous phase transitions. These interdisciplinary transitions exemplify the productivity of such interdisciplinary interactions in science.
Interfacial Molecular Searching Using Forager Dynamics
NASA Astrophysics Data System (ADS)
Monserud, Jon H.; Schwartz, Daniel K.
2016-03-01
Many biological and technological systems employ efficient non-Brownian intermittent search strategies where localized searches alternate with long flights. Coincidentally, molecular species exhibit intermittent behavior at the solid-liquid interface, where periods of slow motion are punctuated by fast flights through the liquid phase. Single-molecule tracking was used here to observe the interfacial search process of DNA for complementary DNA. Measured search times were qualitatively consistent with an intermittent-flight model, and ˜10 times faster than equivalent Brownian searches, suggesting that molecular searches for reactive sites benefit from similar efficiencies as biological organisms.
Dynamics of molecular superrotors in an external magnetic field
NASA Astrophysics Data System (ADS)
Korobenko, Aleksey; Milner, Valery
2015-08-01
We excite diatomic oxygen and nitrogen to high rotational states with an optical centrifuge and study their dynamics in an external magnetic field. Ion imaging is employed to directly visualize, and follow in time, the rotation plane of the molecular superrotors. The two different mechanisms of interaction between the magnetic field and the molecular angular momentum in paramagnetic oxygen and non-magnetic nitrogen lead to qualitatively different behaviour. In nitrogen, we observe the precession of the molecular angular momentum around the field vector. In oxygen, strong spin-rotation coupling results in faster and richer dynamics, encompassing the splitting of the rotation plane into three separate components. As the centrifuged molecules evolve with no significant dispersion of the molecular wave function, the observed magnetic interaction presents an efficient mechanism for controlling the plane of molecular rotation.
Timr, Štěpán; Brabec, Jiří; Bondar, Alexey; Ryba, Tomáš; Železný, Miloš; Lazar, Josef; Jungwirth, Pavel
2015-07-30
Several methods based on single- and two-photon fluorescence detected linear dichroism have recently been used to determine the orientational distributions of fluorescent dyes in lipid membranes. However, these determinations relied on simplified descriptions of nonlinear anisotropic properties of the dye molecules, using a transition dipole-moment-like vector instead of an absorptivity tensor. To investigate the validity of the vector approximation, we have now carried out a combination of computer simulations and polarization microscopy experiments on two representative fluorescent dyes (DiI and F2N12S) embedded in aqueous phosphatidylcholine bilayers. Our results indicate that a simplified vector-like treatment of the two-photon transition tensor is applicable for molecular geometries sampled in the membrane at ambient conditions. Furthermore, our results allow evaluation of several distinct polarization microscopy techniques. In combination, our results point to a robust and accurate experimental and computational treatment of orientational distributions of DiI, F2N12S, and related dyes (including Cy3, Cy5, and others), with implications to monitoring physiologically relevant processes in cellular membranes in a novel way.
Flynn, Jullien M; Brown, Emily A; Chain, Frédéric J J; MacIsaac, Hugh J; Cristescu, Melania E
2015-01-01
Metabarcoding has the potential to become a rapid, sensitive, and effective approach for identifying species in complex environmental samples. Accurate molecular identification of species depends on the ability to generate operational taxonomic units (OTUs) that correspond to biological species. Due to the sometimes enormous estimates of biodiversity using this method, there is a great need to test the efficacy of data analysis methods used to derive OTUs. Here, we evaluate the performance of various methods for clustering length variable 18S amplicons from complex samples into OTUs using a mock community and a natural community of zooplankton species. We compare analytic procedures consisting of a combination of (1) stringent and relaxed data filtering, (2) singleton sequences included and removed, (3) three commonly used clustering algorithms (mothur, UCLUST, and UPARSE), and (4) three methods of treating alignment gaps when calculating sequence divergence. Depending on the combination of methods used, the number of OTUs varied by nearly two orders of magnitude for the mock community (60–5068 OTUs) and three orders of magnitude for the natural community (22–22191 OTUs). The use of relaxed filtering and the inclusion of singletons greatly inflated OTU numbers without increasing the ability to recover species. Our results also suggest that the method used to treat gaps when calculating sequence divergence can have a great impact on the number of OTUs. Our findings are particularly relevant to studies that cover taxonomically diverse species and employ markers such as rRNA genes in which length variation is extensive. PMID:26078860
Kelly, Aaron; Markland, Thomas E.; Brackbill, Nora
2015-03-07
In this article, we show how Ehrenfest mean field theory can be made both a more accurate and efficient method to treat nonadiabatic quantum dynamics by combining it with the generalized quantum master equation framework. The resulting mean field generalized quantum master equation (MF-GQME) approach is a non-perturbative and non-Markovian theory to treat open quantum systems without any restrictions on the form of the Hamiltonian that it can be applied to. By studying relaxation dynamics in a wide range of dynamical regimes, typical of charge and energy transfer, we show that MF-GQME provides a much higher accuracy than a direct application of mean field theory. In addition, these increases in accuracy are accompanied by computational speed-ups of between one and two orders of magnitude that become larger as the system becomes more nonadiabatic. This combination of quantum-classical theory and master equation techniques thus makes it possible to obtain the accuracy of much more computationally expensive approaches at a cost lower than even mean field dynamics, providing the ability to treat the quantum dynamics of atomistic condensed phase systems for long times.
Kelly, Aaron; Brackbill, Nora; Markland, Thomas E
2015-03-01
In this article, we show how Ehrenfest mean field theory can be made both a more accurate and efficient method to treat nonadiabatic quantum dynamics by combining it with the generalized quantum master equation framework. The resulting mean field generalized quantum master equation (MF-GQME) approach is a non-perturbative and non-Markovian theory to treat open quantum systems without any restrictions on the form of the Hamiltonian that it can be applied to. By studying relaxation dynamics in a wide range of dynamical regimes, typical of charge and energy transfer, we show that MF-GQME provides a much higher accuracy than a direct application of mean field theory. In addition, these increases in accuracy are accompanied by computational speed-ups of between one and two orders of magnitude that become larger as the system becomes more nonadiabatic. This combination of quantum-classical theory and master equation techniques thus makes it possible to obtain the accuracy of much more computationally expensive approaches at a cost lower than even mean field dynamics, providing the ability to treat the quantum dynamics of atomistic condensed phase systems for long times.
Xu, Z N; Wang, S Y
2015-02-01
To improve the accuracy in the calculation of dynamic contact angle for drops on the inclined surface, a significant number of numerical drop profiles on the inclined surface with different inclination angles, drop volumes, and contact angles are generated based on the finite difference method, a least-squares ellipse-fitting algorithm is used to calculate the dynamic contact angle. The influences of the above three factors are systematically investigated. The results reveal that the dynamic contact angle errors, including the errors of the left and right contact angles, evaluated by the ellipse-fitting algorithm tend to increase with inclination angle/drop volume/contact angle. If the drop volume and the solid substrate are fixed, the errors of the left and right contact angles increase with inclination angle. After performing a tremendous amount of computation, the critical dimensionless drop volumes corresponding to the critical contact angle error are obtained. Based on the values of the critical volumes, a highly accurate dynamic contact angle algorithm is proposed and fully validated. Within nearly the whole hydrophobicity range, it can decrease the dynamic contact angle error in the inclined plane method to less than a certain value even for different types of liquids.
Wang, Junmei; Tingjun, Hou
2011-01-01
Molecular mechanical force field (FF) methods are useful in studying condensed phase properties. They are complementary to experiment and can often go beyond experiment in atomic details. Even a FF is specific for studying structures, dynamics and functions of biomolecules, it is still important for the FF to accurately reproduce the experimental liquid properties of small molecules that represent the chemical moieties of biomolecules. Otherwise, the force field may not describe the structures and energies of macromolecules in aqueous solutions properly. In this work, we have carried out a systematic study to evaluate the General AMBER Force Field (GAFF) in studying densities and heats of vaporization for a large set of organic molecules that covers the most common chemical functional groups. The latest techniques, such as the particle mesh Ewald (PME) for calculating electrostatic energies, and Langevin dynamics for scaling temperatures, have been applied in the molecular dynamics (MD) simulations. For density, the average percent error (APE) of 71 organic compounds is 4.43% when compared to the experimental values. More encouragingly, the APE drops to 3.43% after the exclusion of two outliers and four other compounds for which the experimental densities have been measured with pressures higher than 1.0 atm. For heat of vaporization, several protocols have been investigated and the best one, P4/ntt0, achieves an average unsigned error (AUE) and a root-mean-square error (RMSE) of 0.93 and 1.20 kcal/mol, respectively. How to reduce the prediction errors through proper van der Waals (vdW) parameterization has been discussed. An encouraging finding in vdW parameterization is that both densities and heats of vaporization approach their “ideal” values in a synchronous fashion when vdW parameters are tuned. The following hydration free energy calculation using thermodynamic integration further justifies the vdW refinement. We conclude that simple vdW parameterization
Luo, Ye Sorella, Sandro; Zen, Andrea
2014-11-21
We present a systematic study of a recently developed ab initio simulation scheme based on molecular dynamics and quantum Monte Carlo. In this approach, a damped Langevin molecular dynamics is employed by using a statistical evaluation of the forces acting on each atom by means of quantum Monte Carlo. This allows the use of an highly correlated wave function parametrized by several variational parameters and describing quite accurately the Born-Oppenheimer energy surface, as long as these parameters are determined at the minimum energy condition. However, in a statistical method both the minimization method and the evaluation of the atomic forces are affected by the statistical noise. In this work, we study systematically the accuracy and reliability of this scheme by targeting the vibrational frequencies of simple molecules such as the water monomer, hydrogen sulfide, sulfur dioxide, ammonia, and phosphine. We show that all sources of systematic errors can be controlled and reliable frequencies can be obtained with a reasonable computational effort. This work provides convincing evidence that this molecular dynamics scheme can be safely applied also to realistic systems containing several atoms.
First principles molecular dynamics without self-consistent field optimization
Souvatzis, Petros; Niklasson, Anders M. N.
2014-01-28
We present a first principles molecular dynamics approach that is based on time-reversible extended Lagrangian Born-Oppenheimer molecular dynamics [A. M. N. Niklasson, Phys. Rev. Lett. 100, 123004 (2008)] in the limit of vanishing self-consistent field optimization. The optimization-free dynamics keeps the computational cost to a minimum and typically provides molecular trajectories that closely follow the exact Born-Oppenheimer potential energy surface. Only one single diagonalization and Hamiltonian (or Fockian) construction are required in each integration time step. The proposed dynamics is derived for a general free-energy potential surface valid at finite electronic temperatures within hybrid density functional theory. Even in the event of irregular functional behavior that may cause a dynamical instability, the optimization-free limit represents a natural starting guess for force calculations that may require a more elaborate iterative electronic ground state optimization. Our optimization-free dynamics thus represents a flexible theoretical framework for a broad and general class of ab initio molecular dynamics simulations.
Georgescu, Ionut; Deckman, Jason; Fredrickson, Laura J; Mandelshtam, Vladimir A
2011-05-01
A new method, here called thermal Gaussian molecular dynamics (TGMD), for simulating the dynamics of quantum many-body systems has recently been introduced [I. Georgescu and V. A. Mandelshtam, Phys. Rev. B 82, 094305 (2010)]. As in the centroid molecular dynamics (CMD), in TGMD the N-body quantum system is mapped to an N-body classical system. The associated both effective Hamiltonian and effective force are computed within the variational Gaussian wave-packet approximation. The TGMD is exact for the high-temperature limit, accurate for short times, and preserves the quantum canonical distribution. For a harmonic potential and any form of operator Â, it provides exact time correlation functions C(AB)(t) at least for the case of B, a linear combination of the position, x, and momentum, p, operators. While conceptually similar to CMD and other quantum molecular dynamics approaches, the great advantage of TGMD is its computational efficiency. We introduce the many-body implementation and demonstrate it on the benchmark problem of calculating the velocity time auto-correlation function for liquid para-hydrogen, using a system of up to N = 2592 particles. PMID:21548675
Guo, Lifen; Han, Huixian; Ma, Jianyi; Guo, Hua
2015-08-01
Vinylidene is a high-energy isomer of acetylene, and the rearrangement of bonds in the two species serves as a prototype for isomerization reactions. Here, a full-dimensional quantum mechanical study of the vinylidene vibration is carried out on a recently developed global acetylene-vinylidene potential energy surface by simulating the photodetachment dynamics of the vinylidene anion. Several low-lying vibrational levels of the anion were first determined on a new ab initio based potential energy surface, and their photoelectron spectra were obtained within the Condon approximation. The vibrational features of the vinylidene isomer are found to agree well with the experiment in both positions and intensities, validating the global acetylene-vinylidene potential energy surface.
VUV studies of molecular photofragmentation dynamics
White, M.G.
1993-12-01
State-resolved, photoion and photoelectron methods are used to study the neutral fragmentation and ionization dynamics of small molecules relevant to atmospheric and combustion chemistry. Photodissociation and ionization are initiated by coherent VUV radiation and the fragmentation dynamics are extracted from measurements of product rovibronic state distributions, kinetic energies and angular distributions. The general aim of these studies is to investigate the multichannel interactions between the electronic and nuclear motions which determine the evolution of the photoexcited {open_quotes}complex{close_quotes} into the observed asymptotic channels.
Time-Accurate Computational Fluid Dynamics Simulation of a Pair of Moving Solid Rocket Boosters
NASA Technical Reports Server (NTRS)
Strutzenberg, Louise L.; Williams, Brandon R.
2011-01-01
Since the Columbia accident, the threat to the Shuttle launch vehicle from debris during the liftoff timeframe has been assessed by the Liftoff Debris Team at NASA/MSFC. In addition to engineering methods of analysis, CFD-generated flow fields during the liftoff timeframe have been used in conjunction with 3-DOF debris transport methods to predict the motion of liftoff debris. Early models made use of a quasi-steady flow field approximation with the vehicle positioned at a fixed location relative to the ground; however, a moving overset mesh capability has recently been developed for the Loci/CHEM CFD software which enables higher-fidelity simulation of the Shuttle transient plume startup and liftoff environment. The present work details the simulation of the launch pad and mobile launch platform (MLP) with truncated solid rocket boosters (SRBs) moving in a prescribed liftoff trajectory derived from Shuttle flight measurements. Using Loci/CHEM, time-accurate RANS and hybrid RANS/LES simulations were performed for the timeframe T0+0 to T0+3.5 seconds, which consists of SRB startup to a vehicle altitude of approximately 90 feet above the MLP. Analysis of the transient flowfield focuses on the evolution of the SRB plumes in the MLP plume holes and the flame trench, impingement on the flame deflector, and especially impingment on the MLP deck resulting in upward flow which is a transport mechanism for debris. The results show excellent qualitative agreement with the visual record from past Shuttle flights, and comparisons to pressure measurements in the flame trench and on the MLP provide confidence in these simulation capabilities.
Three-Dimensional Molecular Theory of Solvation Coupled with Molecular Dynamics in Amber
Luchko, T.; Simmerling, C.; Gusarov, S.; Roe, D.R., Case, D.A.; Tuszynski, J.; Kovalenko, A.
2010-02-01
We present the three-dimensional molecular theory of solvation (also known as 3D-RISM) coupled with molecular dynamics (MD) simulation by contracting solvent degrees of freedom, accelerated by extrapolating solvent-induced forces and applying them in large multiple time steps (up to 20 fs) to enable simulation of large biomolecules. The method has been implemented in the Amber molecular modeling package and is illustrated here on alanine-dipeptide and protein-G.
Three-dimensional molecular theory of solvation coupled with molecular dynamics in Amber
Luchko, Tyler; Gusarov, Sergey; Roe, Daniel R.; Simmerling, Carlos; Case, David A.; Tuszynski, Jack; Kovalenko, Andriy
2010-01-01
We present the three-dimensional molecular theory of solvation (also known as 3D-RISM) coupled with molecular dynamics (MD) simulation by contracting solvent degrees of freedom, accelerated by extrapolating solvent-induced forces and applying them in large multi-time steps (up to 20 fs) to enable simulation of large biomolecules. The method has been implemented in the Amber molecular modeling package, and is illustrated here on alanine dipeptide and protein G. PMID:20440377
Multiscale Reactive Molecular Dynamics for Absolute pK a Predictions and Amino Acid Deprotonation.
Nelson, J Gard; Peng, Yuxing; Silverstein, Daniel W; Swanson, Jessica M J
2014-07-01
Accurately calculating a weak acid's pK a from simulations remains a challenging task. We report a multiscale theoretical approach to calculate the free energy profile for acid ionization, resulting in accurate absolute pK a values in addition to insights into the underlying mechanism. Importantly, our approach minimizes empiricism by mapping electronic structure data (QM/MM forces) into a reactive molecular dynamics model capable of extensive sampling. Consequently, the bulk property of interest (the absolute pK a) is the natural consequence of the model, not a parameter used to fit it. This approach is applied to create reactive models of aspartic and glutamic acids. We show that these models predict the correct pK a values and provide ample statistics to probe the molecular mechanism of dissociation. This analysis shows changes in the solvation structure and Zundel-dominated transitions between the protonated acid, contact ion pair, and bulk solvated excess proton. PMID:25061442
Application of JAERI quantum molecular dynamics model for collisions of heavy nuclei
NASA Astrophysics Data System (ADS)
Ogawa, Tatsuhiko; Hashimoto, Shintaro; Sato, Tatsuhiko; Niita, Koji
2016-06-01
The quantum molecular dynamics (QMD) model incorporated into the general-purpose radiation transport code PHITS was revised for accurate prediction of fragment yields in peripheral collisions. For more accurate simulation of peripheral collisions, stability of the nuclei at their ground state was improved and the algorithm to reject invalid events was modified. In-medium correction on nucleon-nucleon cross sections was also considered. To clarify the effect of this improvement on fragmentation of heavy nuclei, the new QMD model coupled with a statistical decay model was used to calculate fragment production cross sections of Ag and Au targets and compared with the data of earlier measurement. It is shown that the revised version can predict cross section more accurately.
Dynamic Bayesian Network for Accurate Detection of Peptides from Tandem Mass Spectra.
Halloran, John T; Bilmes, Jeff A; Noble, William S
2016-08-01
A central problem in mass spectrometry analysis involves identifying, for each observed tandem mass spectrum, the corresponding generating peptide. We present a dynamic Bayesian network (DBN) toolkit that addresses this problem by using a machine learning approach. At the heart of this toolkit is a DBN for Rapid Identification (DRIP), which can be trained from collections of high-confidence peptide-spectrum matches (PSMs). DRIP's score function considers fragment ion matches using Gaussians rather than fixed fragment-ion tolerances and also finds the optimal alignment between the theoretical and observed spectrum by considering all possible alignments, up to a threshold that is controlled using a beam-pruning algorithm. This function not only yields state-of-the art database search accuracy but also can be used to generate features that significantly boost the performance of the Percolator postprocessor. The DRIP software is built upon a general purpose DBN toolkit (GMTK), thereby allowing a wide variety of options for user-specific inference tasks as well as facilitating easy modifications to the DRIP model in future work. DRIP is implemented in Python and C++ and is available under Apache license at http://melodi-lab.github.io/dripToolkit .
Dynamic Bayesian Network for Accurate Detection of Peptides from Tandem Mass Spectra.
Halloran, John T; Bilmes, Jeff A; Noble, William S
2016-08-01
A central problem in mass spectrometry analysis involves identifying, for each observed tandem mass spectrum, the corresponding generating peptide. We present a dynamic Bayesian network (DBN) toolkit that addresses this problem by using a machine learning approach. At the heart of this toolkit is a DBN for Rapid Identification (DRIP), which can be trained from collections of high-confidence peptide-spectrum matches (PSMs). DRIP's score function considers fragment ion matches using Gaussians rather than fixed fragment-ion tolerances and also finds the optimal alignment between the theoretical and observed spectrum by considering all possible alignments, up to a threshold that is controlled using a beam-pruning algorithm. This function not only yields state-of-the art database search accuracy but also can be used to generate features that significantly boost the performance of the Percolator postprocessor. The DRIP software is built upon a general purpose DBN toolkit (GMTK), thereby allowing a wide variety of options for user-specific inference tasks as well as facilitating easy modifications to the DRIP model in future work. DRIP is implemented in Python and C++ and is available under Apache license at http://melodi-lab.github.io/dripToolkit . PMID:27397138
Halverson, Thomas; Poirier, Bill
2012-12-14
In a series of earlier articles [B. Poirier, J. Theor. Comput. Chem. 2, 65 (2003); B. Poirier and A. Salam, J. Chem. Phys. 121, 1690 (2004); and ibid. 121, 1704 (2004)], a new method was introduced for performing exact quantum dynamics calculations. The method uses a 'weylet' basis set (orthogonalized Weyl-Heisenberg wavelets) combined with phase space truncation, to defeat the exponential scaling of CPU effort with system dimensionality-the first method ever able to achieve this long-standing goal. Here, we develop another such method, which uses a much more convenient basis of momentum-symmetrized Gaussians. Despite being non-orthogonal, symmetrized Gaussians are collectively local, allowing for effective phase space truncation. A dimension-independent code for computing energy eigenstates of both coupled and uncoupled systems has been created, exploiting massively parallel algorithms. Results are presented for model isotropic uncoupled harmonic oscillators and coupled anharmonic oscillators up to 27 dimensions. These are compared with the previous weylet calculations (uncoupled harmonic oscillators up to 15 dimensions), and found to be essentially just as efficient. Coupled system results are also compared to corresponding exact results obtained using a harmonic oscillator basis, and also to approximate results obtained using first-order perturbation theory up to the maximum dimensionality for which the latter may be feasibly obtained (four dimensions).
Puzzarini, Cristina; Biczysko, Malgorzata; Barone, Vincenzo; Peña, Isabel; Cabezas, Carlos; Alonso, José L
2013-10-21
The computational composite scheme purposely set up for accurately describing the electronic structure and spectroscopic properties of small biomolecules has been applied to the first study of the rotational spectrum of 2-thiouracil. The experimental investigation was made possible thanks to the combination of the laser ablation technique with Fourier transform microwave spectrometers. The joint experimental-computational study allowed us to determine the accurate molecular structure and spectroscopic properties of the title molecule, but more importantly, it demonstrates a reliable approach for the accurate investigation of isolated small biomolecules.
Molecular Mechanotransduction: how forces trigger cytoskeletal dynamics
NASA Astrophysics Data System (ADS)
Ehrlicher, Allen
2012-02-01
Mechanical stresses elicit cellular reactions mediated by chemical signals. Defective responses to forces underlie human medical disorders, such as cardiac failure and pulmonary injury. Despite detailed knowledge of the cytoskeleton's structure, the specific molecular switches that convert mechanical stimuli into chemical signals have remained elusive. Here we identify the actin-binding protein, filamin A (FLNa) as a central mechanotransduction element of the cytoskeleton by using Fluorescence Loss After photoConversion (FLAC), a novel high-speed alternative to FRAP. We reconstituted a minimal system consisting of actin filaments, FLNa and two FLNa-binding partners: the cytoplasmic tail of ß-integrin, and FilGAP. Integrins form an essential mechanical linkage between extracellular and intracellular environments, with ß integrin tails connecting to the actin cytoskeleton by binding directly to filamin. FilGAP is a FLNa-binding GTPase-activating protein specific for Rac, which in vivo regulates cell spreading and bleb formation. We demonstrate that both externally-imposed bulk shear and myosin II driven forces differentially regulate the binding of integrin and FilGAP to FLNa. Consistent with structural predictions, strain increases ß-integrin binding to FLNa, whereas it causes FilGAP to dissociate from FLNa, providing a direct and specific molecular basis for cellular mechanotransduction. These results identify the first molecular mechanotransduction element within the actin cytoskeleton, revealing that mechanical strain of key proteins regulates the binding of signaling molecules. Moreover, GAP activity has been shown to switch cell movement from mesenchymal to amoeboid motility, suggesting that mechanical forces directly impact the invasiveness of cancer.
Pseudorotational Dynamics of Small Molecular Systems
NASA Astrophysics Data System (ADS)
Hagelberg, Frank
2001-03-01
A variety of dynamic effects related to the pseudorotation of triatomic singly charged species is explored using the Electron Nuclear Dynamics(END)Theory. The concepts relevant to the motion studied are developed through the analysis of the simplest polyatomic molecule, namely H3+. It is shown that the limiting situation of circular pseudorotation is unattainable for this case. This observation is explained by the anisotropy of the ground state potential energy surface caused by the interaction between the D3h ground state of the molecule and its twofold degenerate first excited state. Further, pseudorotational motion is demonstrated to induce a rotational mode which in turn couples the two shape oscillation modes by action of the Coriolis force. Analogous phenomena are found for Li3+. The Jahn-Teller system C3+ exhibits a range of new motional effects. Particularly, a characteristic frequency shift between the two shape oscillation modes is obtained, resulting from the anisotropy in the curvature of the C2v minimum of C3+. The Jahn-Teller parameters of the system are determined from Electron Nuclear Dynamics simulations.
Hydrolysis of Al3+ from constrained molecular dynamics
NASA Astrophysics Data System (ADS)
Ikeda, Takashi; Hirata, Masaru; Kimura, Takaumi
2006-02-01
We investigated the hydrolysis reactions of Al3+ in AlCl3 aqueous solution using the constrained molecular dynamics based on the Car-Parrinello molecular-dynamics method. By employing the proton-aluminum coordination number as a reaction coordinate in the constrained molecular dynamics the deprotonation as well as dehydration processes are successfully realized. From our free-energy difference of ΔG0≃8.0kcalmol-1 the hydrolysis constant pKa1 is roughly estimated as 5.8, comparable to the literature value of 5.07. We show that the free-energy difference for the hydrolysis of Al3+ in acidic conditions is at least 4kcalmol-1 higher than that in neutral condition, indicating that the hydrolysis reaction is inhibited by the presence of excess protons located around the hydrated ion, in agreement with the change of the predominant species by pH.
Molecular dynamics insights into human aquaporin 2 water channel.
Binesh, A R; Kamali, R
2015-12-01
In this study, the first molecular dynamics simulation of the human aquaporin 2 is performed and for a better understanding of the aquaporin 2 permeability performance, the characteristics of water transport in this protein channel and key biophysical parameters of AQP2 tetramer including osmotic and diffusive permeability constants and the pore radius are investigated. For this purpose, recently recovered high resolution X-ray crystal structure of` the human aquaporin 2 is used to perform twenty nanosecond molecular dynamics simulation of fully hydrated tetramer of this protein embedded in a lipid bilayer. The resulting water permeability characteristics of this protein channel showed that the water permeability of the human AQP2 is in a mean range in comparison with other human aquaporins family. Finally, the results reported in this research demonstrate that molecular dynamics simulation of human AQP2 provided useful insights into the mechanisms of water permeation and urine concentration in the human kidney. PMID:26489820
Theoretical Analysis of Dynamic Processes for Interacting Molecular Motors
Teimouri, Hamid; Kolomeisky, Anatoly B.; Mehrabiani, Kareem
2015-01-01
Biological transport is supported by collective dynamics of enzymatic molecules that are called motor proteins or molecular motors. Experiments suggest that motor proteins interact locally via short-range potentials. We investigate the fundamental role of these interactions by analyzing a new class of totally asymmetric exclusion processes where interactions are accounted for in a thermodynamically consistent fashion. It allows us to connect explicitly microscopic features of motor proteins with their collective dynamic properties. Theoretical analysis that combines various mean-field calculations and computer simulations suggests that dynamic properties of molecular motors strongly depend on interactions, and correlations are stronger for interacting motor proteins. Surprisingly, it is found that there is an optimal strength of interactions (weak repulsion) that leads to a maximal particle flux. It is also argued that molecular motors transport is more sensitive to attractive interactions. Applications of these results for kinesin motor proteins are discussed. PMID:25688287
Molecular dynamics insights into human aquaporin 2 water channel.
Binesh, A R; Kamali, R
2015-12-01
In this study, the first molecular dynamics simulation of the human aquaporin 2 is performed and for a better understanding of the aquaporin 2 permeability performance, the characteristics of water transport in this protein channel and key biophysical parameters of AQP2 tetramer including osmotic and diffusive permeability constants and the pore radius are investigated. For this purpose, recently recovered high resolution X-ray crystal structure of` the human aquaporin 2 is used to perform twenty nanosecond molecular dynamics simulation of fully hydrated tetramer of this protein embedded in a lipid bilayer. The resulting water permeability characteristics of this protein channel showed that the water permeability of the human AQP2 is in a mean range in comparison with other human aquaporins family. Finally, the results reported in this research demonstrate that molecular dynamics simulation of human AQP2 provided useful insights into the mechanisms of water permeation and urine concentration in the human kidney.
Thermal Conductivity of Natural Rubber Using Molecular Dynamics Simulation.
He, Yan; Ma, Lian-Xiang; Tang, Yuan-Zheng; Wang, Ze-Peng; Li, Wei; Kukulka, David
2015-04-01
Thermal conductivity of natural rubber has been studied by classic molecular dynamics simulations. These simulations are performed on natural rubber models using the adaptive intermolecular reactive empirical bond order (AIREBO) and the Green-Kubo molecular dynamics (MD) simulations. Thermal conductivity results are found to be very sensitive to the time step used in the simulations. For a time step of 0.1 fs, the converged thermal conductivity is 0.35 W/mK. Additionally the anisotropic thermal conductivity of a specially-modeled natural rubber model with straight molecular chains was studied and values of thermal conductivity parallel to the molecular chains was found to be 1.71 W/mK and the anisotropy, 2Kz/(Kx + Ky), was 2.67.
Modeling ramp compression experiments using large-scale molecular dynamics simulation.
Mattsson, Thomas Kjell Rene; Desjarlais, Michael Paul; Grest, Gary Stephen; Templeton, Jeremy Alan; Thompson, Aidan Patrick; Jones, Reese E.; Zimmerman, Jonathan A.; Baskes, Michael I.; Winey, J. Michael; Gupta, Yogendra Mohan; Lane, J. Matthew D.; Ditmire, Todd; Quevedo, Hernan J.
2011-10-01
Molecular dynamics simulation (MD) is an invaluable tool for studying problems sensitive to atomscale physics such as structural transitions, discontinuous interfaces, non-equilibrium dynamics, and elastic-plastic deformation. In order to apply this method to modeling of ramp-compression experiments, several challenges must be overcome: accuracy of interatomic potentials, length- and time-scales, and extraction of continuum quantities. We have completed a 3 year LDRD project with the goal of developing molecular dynamics simulation capabilities for modeling the response of materials to ramp compression. The techniques we have developed fall in to three categories (i) molecular dynamics methods (ii) interatomic potentials (iii) calculation of continuum variables. Highlights include the development of an accurate interatomic potential describing shock-melting of Beryllium, a scaling technique for modeling slow ramp compression experiments using fast ramp MD simulations, and a technique for extracting plastic strain from MD simulations. All of these methods have been implemented in Sandia's LAMMPS MD code, ensuring their widespread availability to dynamic materials research at Sandia and elsewhere.
Studying Interactions by Molecular Dynamics Simulations at High Concentration
Fogolari, Federico; Corazza, Alessandra; Toppo, Stefano; Tosatto, Silvio C. E.; Viglino, Paolo; Ursini, Fulvio; Esposito, Gennaro
2012-01-01
Molecular dynamics simulations have been used to study molecular encounters and recognition. In recent works, simulations using high concentration of interacting molecules have been performed. In this paper, we consider the practical problems for setting up the simulation and to analyse the results of the simulation. The simulation of beta 2-microglobulin association and the simulation of the binding of hydrogen peroxide by glutathione peroxidase are provided as examples. PMID:22500085
State-to-state dynamics of molecular energy transfer
Gentry, W.R.; Giese, C.F.
1993-12-01
The goal of this research program is to elucidate the elementary dynamical mechanisms of vibrational and rotational energy transfer between molecules, at a quantum-state resolved level of detail. Molecular beam techniques are used to isolate individual molecular collisions, and to control the kinetic energy of collision. Lasers are used both to prepare specific quantum states prior to collision by stimulated-emission pumping (SEP), and to measure the distribution of quantum states in the collision products by laser-induced fluorescence (LIF). The results are interpreted in terms of dynamical models, which may be cast in a classical, semiclassical or quantum mechanical framework, as appropriate.
AceCloud: Molecular Dynamics Simulations in the Cloud.
Harvey, M J; De Fabritiis, G
2015-05-26
We present AceCloud, an on-demand service for molecular dynamics simulations. AceCloud is designed to facilitate the secure execution of large ensembles of simulations on an external cloud computing service (currently Amazon Web Services). The AceCloud client, integrated into the ACEMD molecular dynamics package, provides an easy-to-use interface that abstracts all aspects of interaction with the cloud services. This gives the user the experience that all simulations are running on their local machine, minimizing the learning curve typically associated with the transition to using high performance computing services.
How Dynamic Visualization Technology can Support Molecular Reasoning
NASA Astrophysics Data System (ADS)
Levy, Dalit
2012-11-01
This paper reports the results of a study aimed at exploring the advantages of dynamic visualization for the development of better understanding of molecular processes. We designed a technology-enhanced curriculum module in which high school chemistry students conduct virtual experiments with dynamic molecular visualizations of solid, liquid, and gas. They interact with the visualizations and carry out inquiry activities to make and refine connections between observable phenomena and atomic level processes related to phase change. The explanations proposed by 300 pairs of students in response to pre/post-assessment items have been analyzed using a scale for measuring the level of molecular reasoning. Results indicate that from pretest to posttest, students make progress in their level of molecular reasoning and are better able to connect intermolecular forces and phase change in their explanations. The paper presents the results through the lens of improvement patterns and the metaphor of the "ladder of molecular reasoning," and discusses how this adds to our understanding of the benefits of interacting with dynamic molecular visualizations.
Multiple time step integrators in ab initio molecular dynamics
Luehr, Nathan; Martínez, Todd J.; Markland, Thomas E.
2014-02-28
Multiple time-scale algorithms exploit the natural separation of time-scales in chemical systems to greatly accelerate the efficiency of molecular dynamics simulations. Although the utility of these methods in systems where the interactions are described by empirical potentials is now well established, their application to ab initio molecular dynamics calculations has been limited by difficulties associated with splitting the ab initio potential into fast and slowly varying components. Here we present two schemes that enable efficient time-scale separation in ab initio calculations: one based on fragment decomposition and the other on range separation of the Coulomb operator in the electronic Hamiltonian. We demonstrate for both water clusters and a solvated hydroxide ion that multiple time-scale molecular dynamics allows for outer time steps of 2.5 fs, which are as large as those obtained when such schemes are applied to empirical potentials, while still allowing for bonds to be broken and reformed throughout the dynamics. This permits computational speedups of up to 4.4x, compared to standard Born-Oppenheimer ab initio molecular dynamics with a 0.5 fs time step, while maintaining the same energy conservation and accuracy.
Electron-phonon interaction within classical molecular dynamics
Tamm, A.; Samolyuk, G.; Correa, A. A.; Klintenberg, M.; Aabloo, A.; Caro, A.
2016-07-14
Here, we present a model for nonadiabatic classical molecular dynamics simulations that captures with high accuracy the wave-vector q dependence of the phonon lifetimes, in agreement with quantum mechanics calculations. It is based on a local view of the e-ph interaction where individual atom dynamics couples to electrons via a damping term that is obtained as the low-velocity limit of the stopping power of a moving ion in a host. The model is parameter free, as its components are derived from ab initio-type calculations, is readily extended to the case of alloys, and is adequate for large-scale molecular dynamics computermore » simulations. We also show how this model removes some oversimplifications of the traditional ionic damped dynamics commonly used to describe situations beyond the Born-Oppenheimer approximation.« less
Electron-phonon interaction within classical molecular dynamics
NASA Astrophysics Data System (ADS)
Tamm, A.; Samolyuk, G.; Correa, A. A.; Klintenberg, M.; Aabloo, A.; Caro, A.
2016-07-01
We present a model for nonadiabatic classical molecular dynamics simulations that captures with high accuracy the wave-vector q dependence of the phonon lifetimes, in agreement with quantum mechanics calculations. It is based on a local view of the e -ph interaction where individual atom dynamics couples to electrons via a damping term that is obtained as the low-velocity limit of the stopping power of a moving ion in a host. The model is parameter free, as its components are derived from ab initio-type calculations, is readily extended to the case of alloys, and is adequate for large-scale molecular dynamics computer simulations. We also show how this model removes some oversimplifications of the traditional ionic damped dynamics commonly used to describe situations beyond the Born-Oppenheimer approximation.
Molecular dynamics simulations of ubiquinone; a survey over torsional potentials and hydrogen bonds
NASA Astrophysics Data System (ADS)
Nilsson, J. Arvid; Lyubartsev, Alexander; Eriksson, Leif A.; Laaksonen, Aatto
Molecular dynamics simulations, both classical and Car-Parrinello, have been carried out to investigate ubiquinone (UQ), a proton mediator in both oxidative and photo-phosphorylation. The main objectives have been to follow the dynamics of methoxy groups, conformation of the tail with respect to the ring, hydration and hydrogen bond structure around UQ. The methoxy groups are found to be able to rotate fairly freely. The tail in both UQ and UQ - is approximately perpendicular to the ring plane. Only weak hydrogen bonds are formed between the neutral form of ubiquinone and water molecules in the solvent, while the anionic form shows a distinct solute-solvent hydrogen bond structure. We also conclude that anionic UQ can be accurately modelled by molecular mechanics methods, but the conformation of the methoxy groups in neutral UQ can hardly be properly modelled using a standard force field.
Restoring electronic coherence/decoherence for a trajectory-based nonadiabatic molecular dynamics
Zhu, Chaoyuan
2016-01-01
By utilizing the time-independent semiclassical phase integral, we obtained modified coupled time-dependent Schrödinger equations that restore coherences and induce decoherences within original simple trajectory-based nonadiabatic molecular dynamic algorithms. Nonadiabatic transition probabilities simulated from both Tully’s fewest switches and semiclassical Ehrenfest algorithms follow exact quantum electronic oscillations and amplitudes for three out of the four well-known model systems. Within the present theory, nonadiabatic transitions estimated from statistical ensemble of trajectories accurately follow those of the modified electronic wave functions. The present theory can be immediately applied to the molecular dynamic simulations of photochemical and photophysical processes involving electronic excited states. PMID:27063337
Self-consistent field theory based molecular dynamics with linear system-size scaling
Richters, Dorothee; Kühne, Thomas D.
2014-04-07
We present an improved field-theoretic approach to the grand-canonical potential suitable for linear scaling molecular dynamics simulations using forces from self-consistent electronic structure calculations. It is based on an exact decomposition of the grand canonical potential for independent fermions and does neither rely on the ability to localize the orbitals nor that the Hamilton operator is well-conditioned. Hence, this scheme enables highly accurate all-electron linear scaling calculations even for metallic systems. The inherent energy drift of Born-Oppenheimer molecular dynamics simulations, arising from an incomplete convergence of the self-consistent field cycle, is circumvented by means of a properly modified Langevin equation. The predictive power of the present approach is illustrated using the example of liquid methane under extreme conditions.
Self-consistent field theory based molecular dynamics with linear system-size scaling.
Richters, Dorothee; Kühne, Thomas D
2014-04-01
We present an improved field-theoretic approach to the grand-canonical potential suitable for linear scaling molecular dynamics simulations using forces from self-consistent electronic structure calculations. It is based on an exact decomposition of the grand canonical potential for independent fermions and does neither rely on the ability to localize the orbitals nor that the Hamilton operator is well-conditioned. Hence, this scheme enables highly accurate all-electron linear scaling calculations even for metallic systems. The inherent energy drift of Born-Oppenheimer molecular dynamics simulations, arising from an incomplete convergence of the self-consistent field cycle, is circumvented by means of a properly modified Langevin equation. The predictive power of the present approach is illustrated using the example of liquid methane under extreme conditions.
Coarse-Grained Molecular Dynamics: Dissipation Due to Internal Modes
Rudd, R E
2001-12-21
We describe progress on the issue of pathological elastic wave reflection in atomistic and multiscale simulation. First we briefly review Coarse-Grained Molecular Dynamics (CGMD). Originally CGMD was formulated as a Hamiltonian system in which energy is conserved. This formulation is useful for many applications, but recently CGMD has been extended to include generalized Langevin forces. Here we describe how Langevin dynamics arise naturally in CGMD, and we examine the implication for elastic wave scattering.
Plastic dislocation motion via nonequilibrium molecular and continuum dynamics
Hoover, W.G.; Ladd, A.J.C.; Hoover, N.E.
1980-09-29
The classical two-dimensional close-packed triangular lattice, with nearest-neighbor spring forces, is a convenient standard material for the investigation of dislocation motion and plastic flow. Two kinds of calculations, based on this standard material, are described here: (1) Molecular Dynamics simulations, incorporating adiabatic strains described with the help of Doll's Tensor, and (2) Continuum Dynamics simulations, incorporating periodic boundaries and dislocation interaction through stress-field superposition.
Input File Creation for the Molecular Dynamics Program LAMMPS.
2001-05-30
The program creates an input data file for the molecular dynamics program LAMMPS. The input file created is a liquid mixture between two walls explicitly composed of particles. The liquid molecules are modeled as a bead-spring molecule. The input data file specifies the position and topology of the starting state. The data structure of input allows for dynamic bond creation (cross-linking) within the LAMMPS code.
Imaging the molecular dynamics of dissociative electron attachment to water
Adaniya, Hidihito; Rudek, B.; Osipov, Timur; Haxton, Dan; Weber, Thorsten; Rescigno, Thomas N.; McCurdy, C.W.; Belkacem, Ali
2009-10-19
Momentum imaging experiments on dissociative electron attachment to the water molecule are combined with ab initio theoretical calculations of the angular dependence of the quantum mechanical amplitude for electron attachment to provide a detailed picture of the molecular dynamics of dissociation attachment via the two lowest energy Feshbach resonances. The combination of momentum imaging experiments and theory can reveal dissociation dynamics for which the axial recoil approximation breaks down and thus provides a powerful reaction microscope for DEA to polyatomics.
NASA Astrophysics Data System (ADS)
Shimizu, Futoshi; Kimizuka, Hajime; Kaburaki, Hideo
2002-08-01
A new parallel computing environment, called as ``Parallel Molecular Dynamics Stencil'', has been developed to carry out a large-scale short-range molecular dynamics simulation of solids. The stencil is written in C language using MPI for parallelization and designed successfully to separate and conceal parts of the programs describing cutoff schemes and parallel algorithms for data communication. This has been made possible by introducing the concept of image atoms. Therefore, only a sequential programming of the force calculation routine is required for executing the stencil in parallel environment. Typical molecular dynamics routines, such as various ensembles, time integration methods, and empirical potentials, have been implemented in the stencil. In the presentation, the performance of the stencil on parallel computers of Hitachi, IBM, SGI, and PC-cluster using the models of Lennard-Jones and the EAM type potentials for fracture problem will be reported.
Molecular dynamics studies of supercooled water using a monatomic model
NASA Astrophysics Data System (ADS)
Moore, Emily Brooke
There remain many unanswered questions regarding the structure and behavior of water, particularly when cooled below the melting temperature into water's supercooled region. In this region, liquid water is metastable, and rapid crystallization makes it difficult to study experimentally the liquid and the crystallization process. Computational studies are hindered by the complexity of accurately modeling water and the computational cost of simulating processes such as crystallization. In this work, the development and validation of mW, a monatomic water model, is presented. This model is able to quantitatively reproduce the structure, dynamic anomalies and phase behavior of water without hydrogen atoms or electrostatics by reproducing water's propensity to form locally tetrahedral structures. Using the mW water model in molecular dynamics simulations, we show the evolution of the local structure of water from 300--100 K. We find that the thermodynamic and structural properties studied, density, tetrahedrality and structural correlation length, change maximally or are maximum at 202 +/- 2 K, the liquid-liquid transformation temperature. Shifting to water confined within cylindrical nanopores, we present the development of a rotationally invariant method, the CHILL algorithm, to distinguish between liquid, hexagonal and cubic ice. We analyze the process of homogeneous nucleation, growth and melting within hydrophilic pores, as well as the effect of water-pore interaction strength on the melting of ice and liquid-ice coexistence within pores. Crystallization within the nanopores results in cubic ice with hexagonal stacking faults in agreement with experiments. We also investigate crystallization of bulk liquid within water's experimentally inaccessible "no man's land." Crystallization occurs through rapid development of ice nuclei that grow and consolidate, precluding the measurement of diffusion within the liquid. Analysis of how ice structure develops shows that
Thermostatted molecular dynamics: How to avoid the Toda demon hidden in Nose-Hoover dynamics
Holian, B.L.; Voter, A.F.; Ravelo, R.
1995-09-01
The Nose-Hoover thermostat, which is often used in the hope of modifying molecular dynamics trajectories in order to achieve canonical-ensemble averages, has hidden in it a Toda ``demon,`` which can give rise to unwanted, noncanonical undulations in the instantaneous kinetic temperature. We show how these long-lived oscillations arise from insufficient coupling of the thermostat to the atoms, and give straightforward, practical procedures for avoiding this weak-coupling pathology in isothermal molecular dynamics simulations.
Molecular circuits for dynamic noise filtering.
Zechner, Christoph; Seelig, Georg; Rullan, Marc; Khammash, Mustafa
2016-04-26
The invention of the Kalman filter is a crowning achievement of filtering theory-one that has revolutionized technology in countless ways. By dealing effectively with noise, the Kalman filter has enabled various applications in positioning, navigation, control, and telecommunications. In the emerging field of synthetic biology, noise and context dependency are among the key challenges facing the successful implementation of reliable, complex, and scalable synthetic circuits. Although substantial further advancement in the field may very well rely on effectively addressing these issues, a principled protocol to deal with noise-as provided by the Kalman filter-remains completely missing. Here we develop an optimal filtering theory that is suitable for noisy biochemical networks. We show how the resulting filters can be implemented at the molecular level and provide various simulations related to estimation, system identification, and noise cancellation problems. We demonstrate our approach in vitro using DNA strand displacement cascades as well as in vivo using flow cytometry measurements of a light-inducible circuit in Escherichia coli. PMID:27078094
Quantum dynamics of light-driven chiral molecular motors.
Yamaki, Masahiro; Nakayama, Shin-ichiro; Hoki, Kunihito; Kono, Hirohiko; Fujimura, Yuichi
2009-03-21
The results of theoretical studies on quantum dynamics of light-driven molecular motors with internal rotation are presented. Characteristic features of chiral motors driven by a non-helical, linearly polarized electric field of light are explained on the basis of symmetry argument. The rotational potential of the chiral motor is characterized by a ratchet form. The asymmetric potential determines the directional motion: the rotational direction is toward the gentle slope of the asymmetric potential. This direction is called the intuitive direction. To confirm the unidirectional rotational motion, results of quantum dynamical calculations of randomly-oriented molecular motors are presented. A theoretical design of the smallest light-driven molecular machine is presented. The smallest chiral molecular machine has an optically driven engine and a running propeller on its body. The mechanisms of transmission of driving forces from the engine to the propeller are elucidated by using a quantum dynamical treatment. The results provide a principle for control of optically-driven molecular bevel gears. Temperature effects are discussed using the density operator formalism. An effective method for ultrafast control of rotational motions in any desired direction is presented with the help of a quantum control theory. In this method, visible or UV light pulses are applied to drive the motor via an electronic excited state. A method for driving a large molecular motor consisting of an aromatic hydrocarbon is presented. The molecular motor is operated by interactions between the induced dipole of the molecular motor and the electric field of light pulses. PMID:19290336
Hayes, Malcolm; Peckova, Kvetoslava; Martinek, Petr; Hora, Milan; Kalusova, Kristyna; Straka, Lubomir; Daum, Ondrej; Kokoskova, Bohuslava; Rotterova, Pavla; Pivovarčikova, Kristyna; Branzovsky, Jindrich; Dubova, Magdalena; Vesela, Pavla; Michal, Michal; Hes, Ondrej
2015-03-01
tumours can only be sub-classified accurately by multi-parameter molecular-genetic analysis. PMID:25544614
Probing Molecular Dynamics by Laser-Induced Backscattering Holography.
Haertelt, Marko; Bian, Xue-Bin; Spanner, Michael; Staudte, André; Corkum, Paul B
2016-04-01
We use differential holography to overcome the forward scattering problem in strong-field photoelectron holography. Our differential holograms of H_{2} and D_{2} molecules exhibit a fishbonelike structure, which arises from the backscattered part of the recolliding photoelectron wave packet. We demonstrate that the backscattering hologram can resolve the different nuclear dynamics between H_{2} and D_{2} with subangstrom spatial and subcycle temporal resolution. In addition, we show that attosecond electron dynamics can be resolved. These results open a new avenue for ultrafast studies of molecular dynamics in small molecules. PMID:27081975
Probing Molecular Dynamics by Laser-Induced Backscattering Holography
NASA Astrophysics Data System (ADS)
Haertelt, Marko; Bian, Xue-Bin; Spanner, Michael; Staudte, André; Corkum, Paul B.
2016-04-01
We use differential holography to overcome the forward scattering problem in strong-field photoelectron holography. Our differential holograms of H2 and D2 molecules exhibit a fishbonelike structure, which arises from the backscattered part of the recolliding photoelectron wave packet. We demonstrate that the backscattering hologram can resolve the different nuclear dynamics between H2 and D2 with subangstrom spatial and subcycle temporal resolution. In addition, we show that attosecond electron dynamics can be resolved. These results open a new avenue for ultrafast studies of molecular dynamics in small molecules.
Optimizing legacy molecular dynamics software with directive-based offload
NASA Astrophysics Data System (ADS)
Michael Brown, W.; Carrillo, Jan-Michael Y.; Gavhane, Nitin; Thakkar, Foram M.; Plimpton, Steven J.
2015-10-01
Directive-based programming models are one solution for exploiting many-core coprocessors to increase simulation rates in molecular dynamics. They offer the potential to reduce code complexity with offload models that can selectively target computations to run on the CPU, the coprocessor, or both. In this paper, we describe modifications to the LAMMPS molecular dynamics code to enable concurrent calculations on a CPU and coprocessor. We demonstrate that standard molecular dynamics algorithms can run efficiently on both the CPU and an x86-based coprocessor using the same subroutines. As a consequence, we demonstrate that code optimizations for the coprocessor also result in speedups on the CPU; in extreme cases up to 4.7X. We provide results for LAMMPS benchmarks and for production molecular dynamics simulations using the Stampede hybrid supercomputer with both Intel® Xeon Phi™ coprocessors and NVIDIA GPUs. The optimizations presented have increased simulation rates by over 2X for organic molecules and over 7X for liquid crystals on Stampede. The optimizations are available as part of the "Intel package" supplied with LAMMPS.
Open boundary molecular dynamics of sheared star-polymer melts.
Sablić, Jurij; Praprotnik, Matej; Delgado-Buscalioni, Rafael
2016-02-28
Open boundary molecular dynamics (OBMD) simulations of a sheared star polymer melt under isothermal conditions are performed to study the rheology and molecular structure of the melt under a fixed normal load. Comparison is made with the standard molecular dynamics (MD) in periodic (closed) boxes at a fixed shear rate (using the SLLOD dynamics). The OBMD system exchanges mass and momentum with adjacent reservoirs (buffers) where the external pressure tensor is imposed. Insertion of molecules in the buffers is made feasible by implementing there a low resolution model (blob-molecules with soft effective interactions) and then using the adaptive resolution scheme (AdResS) to connect with the bulk MD. Straining with increasing shear stress induces melt expansion and a significantly different redistribution of pressure compared with the closed case. In the open sample, the shear viscosity is also a bit lowered but more stable against the viscous heating. At a given Weissenberg number, molecular deformations and material properties (recoverable shear strain and normal stress ratio) are found to be similar in both setups. We also study the modelling effect of normal and tangential friction between monomers implemented in a dissipative particle dynamics (DPD) thermostat. Interestingly, the tangential friction substantially enhances the elastic response of the melt due to a reduction of the kinetic stress viscous contribution. PMID:26820315
Reasoning with Atomic-Scale Molecular Dynamic Models
ERIC Educational Resources Information Center
Pallant, Amy; Tinker, Robert F.
2004-01-01
The studies reported in this paper are an initial effort to explore the applicability of computational models in introductory science learning. Two instructional interventions are described that use a molecular dynamics model embedded in a set of online learning activities with middle and high school students in 10 classrooms. The studies indicate…
Molecular dynamics simulation of size segregation in three dimensions
NASA Astrophysics Data System (ADS)
Gallas, Jason A. C.; Herrmann, Hans J.; Pöschel, Thorsten; Sokołowski, Stefan
1996-01-01
We report the first three-dimensional molecular dynamics simulation of particle segregation by shaking. Two different containers are considered: one cylindrical and another with periodic boundary conditions. The dependence of the time evolution of a test particle inside the material is studied as a function of the shaking frequency and amplitude, damping coefficients, and dispersivity.
Quantum Molecular Dynamics Simulations of Nanotube Tip Assisted Reactions
NASA Technical Reports Server (NTRS)
Menon, Madhu
1998-01-01
In this report we detail the development and application of an efficient quantum molecular dynamics computational algorithm and its application to the nanotube-tip assisted reactions on silicon and diamond surfaces. The calculations shed interesting insights into the microscopic picture of tip surface interactions.
Optimizing legacy molecular dynamics software with directive-based offload
Michael Brown, W.; Carrillo, Jan-Michael Y.; Gavhane, Nitin; Thakkar, Foram M.; Plimpton, Steven J.
2015-05-14
The directive-based programming models are one solution for exploiting many-core coprocessors to increase simulation rates in molecular dynamics. They offer the potential to reduce code complexity with offload models that can selectively target computations to run on the CPU, the coprocessor, or both. In our paper, we describe modifications to the LAMMPS molecular dynamics code to enable concurrent calculations on a CPU and coprocessor. We also demonstrate that standard molecular dynamics algorithms can run efficiently on both the CPU and an x86-based coprocessor using the same subroutines. As a consequence, we demonstrate that code optimizations for the coprocessor also result in speedups on the CPU; in extreme cases up to 4.7X. We provide results for LAMMAS benchmarks and for production molecular dynamics simulations using the Stampede hybrid supercomputer with both Intel (R) Xeon Phi (TM) coprocessors and NVIDIA GPUs: The optimizations presented have increased simulation rates by over 2X for organic molecules and over 7X for liquid crystals on Stampede. The optimizations are available as part of the "Intel package" supplied with LAMMPS. (C) 2015 Elsevier B.V. All rights reserved.
Optimizing legacy molecular dynamics software with directive-based offload
Michael Brown, W.; Carrillo, Jan-Michael Y.; Gavhane, Nitin; Thakkar, Foram M.; Plimpton, Steven J.
2015-05-14
The directive-based programming models are one solution for exploiting many-core coprocessors to increase simulation rates in molecular dynamics. They offer the potential to reduce code complexity with offload models that can selectively target computations to run on the CPU, the coprocessor, or both. In our paper, we describe modifications to the LAMMPS molecular dynamics code to enable concurrent calculations on a CPU and coprocessor. We also demonstrate that standard molecular dynamics algorithms can run efficiently on both the CPU and an x86-based coprocessor using the same subroutines. As a consequence, we demonstrate that code optimizations for the coprocessor also resultmore » in speedups on the CPU; in extreme cases up to 4.7X. We provide results for LAMMAS benchmarks and for production molecular dynamics simulations using the Stampede hybrid supercomputer with both Intel (R) Xeon Phi (TM) coprocessors and NVIDIA GPUs: The optimizations presented have increased simulation rates by over 2X for organic molecules and over 7X for liquid crystals on Stampede. The optimizations are available as part of the "Intel package" supplied with LAMMPS. (C) 2015 Elsevier B.V. All rights reserved.« less
NASA Astrophysics Data System (ADS)
Smith, James Sherwood
A combination of computational chemistry and molecular dynamics (MD) approaches was used to study two polymer-nanoparticle composite (PNPC) systems, first a model bead spring polymer with spherical nanoparticles and generalized interactions, and second, a Poly(dimethylsiloxane) (PDMS)-silica system with accurate quantum chemistry (QC) based force fields. The following molecular processes, which are fundamental to the reinforcement of polymer-nanoparticle composites (PNPC), were studied: (1) the effect of nanoparticle-polymer interactions and polymer molecular weight on nanoparticle dispersion and distribution, (2) the free energy and conformational changes when stretching individual PDMS chains in a melt, and (3) the effect of silica fillers with different surface modifications on the properties of PDMS chains at the interface. In the model PNPC consisting of spherical nanoparticles in a bead-spring polymer melt, it was found that when the polymer-nanoparticle interactions were relatively weak the polymer matrix promoted nanoparticle aggregation. Increasingly attractive nanoparticle-polymer interactions led to strong adsorption of the polymer chains on the surface of the nanoparticles and promoted dispersion of the nanoparticles and were independent of polymer molecular weight. A classical force field for PDMS and its oligomers has been derived on the basis of intermolecular binding energies, molecular geometries, molecular electrostatic potentials, and conformational energies obtained from quantum chemistry calculations and in MD simulations and it accurately reproduces the properties of PDMS melts of various molecular weights. MD simulations using umbrella sampling methods to sample the free energy of stretching a PDMS oligomer in a melt of PDMS oligomers found that the restoring forces were mainly a result of the changes in entropy of the chain as the chain was contracted or stretched, and only at severe extensions did energetic contributions due to deformation
Rational Prediction with Molecular Dynamics for Hit Identification
Nichols, Sara E; Swift, Robert V; Amaro, Rommie E
2012-01-01
Although the motions of proteins are fundamental for their function, for pragmatic reasons, the consideration of protein elasticity has traditionally been neglected in drug discovery and design. This review details protein motion, its relevance to biomolecular interactions and how it can be sampled using molecular dynamics simulations. Within this context, two major areas of research in structure-based prediction that can benefit from considering protein flexibility, binding site detection and molecular docking, are discussed. Basic classification metrics and statistical analysis techniques, which can facilitate performance analysis, are also reviewed. With hardware and software advances, molecular dynamics in combination with traditional structure-based prediction methods can potentially reduce the time and costs involved in the hit identification pipeline. PMID:23110535
Diversity dynamics: molecular phylogenies need the fossil record.
Quental, Tiago B; Marshall, Charles R
2010-08-01
Over the last two decades, new tools in the analysis of molecular phylogenies have enabled study of the diversification dynamics of living clades in the absence of information about extinct lineages. However, computer simulations and the fossil record show that the inability to access extinct lineages severely limits the inferences that can be drawn from molecular phylogenies. It appears that molecular phylogenies can tell us only when there have been changes in diversification rates, but are blind to the true diversity trajectories and rates of origination and extinction that have led to the species that are alive today. We need to embrace the fossil record if we want to fully understand the diversity dynamics of the living biota. PMID:20646780
Collisional dynamics in a gas of molecular super-rotors.
Khodorkovsky, Yuri; Steinitz, Uri; Hartmann, Jean-Michel; Averbukh, Ilya Sh
2015-01-01
Recently, femtosecond laser techniques have been developed that are capable of bringing gas molecules to extremely fast rotation in a very short time, while keeping their translational motion relatively slow. Here we study collisional equilibration dynamics of this new state of molecular gases. We show that the route to equilibrium starts with a metastable 'gyroscopic stage' in the course of which the molecules maintain their fast rotation and orientation of the angular momentum through many collisions. The inhibited rotational-translational relaxation is characterized by a persistent anisotropy in the molecular angular distribution, and is manifested in the optical birefringence and anisotropic diffusion in the gas. After a certain induction time, the 'gyroscopic stage' is abruptly terminated by an explosive rotational-translational energy exchange, leading the gas towards the final equilibrium. We illustrate our conclusions by direct molecular dynamics simulation of several gases of linear molecules. PMID:26160223
Collisional dynamics in a gas of molecular super-rotors
Khodorkovsky, Yuri; Steinitz, Uri; Hartmann, Jean-Michel; Averbukh, Ilya Sh.
2015-01-01
Recently, femtosecond laser techniques have been developed that are capable of bringing gas molecules to extremely fast rotation in a very short time, while keeping their translational motion relatively slow. Here we study collisional equilibration dynamics of this new state of molecular gases. We show that the route to equilibrium starts with a metastable ‘gyroscopic stage' in the course of which the molecules maintain their fast rotation and orientation of the angular momentum through many collisions. The inhibited rotational–translational relaxation is characterized by a persistent anisotropy in the molecular angular distribution, and is manifested in the optical birefringence and anisotropic diffusion in the gas. After a certain induction time, the ‘gyroscopic stage' is abruptly terminated by an explosive rotational–translational energy exchange, leading the gas towards the final equilibrium. We illustrate our conclusions by direct molecular dynamics simulation of several gases of linear molecules. PMID:26160223
Molecular Dynamics Simulations of Lignin Peroxidase in Solution
Francesca Gerini, M.; Roccatano, Danilo; Baciocchi, Enrico; Nola, Alfredo Di
2003-01-01
The dynamical and structural properties of lignin peroxidase and its Trp171Ala mutant have been investigated in aqueous solution using molecular dynamics (MD) simulations. In both cases, the enzyme retained its overall backbone structure and all its noncovalent interactions in the course of the MD simulations. Very interestingly, the analysis of the MD trajectories showed the presence of large fluctuations in correspondence of the residues forming the heme access channel; these movements enlarge the opening and facilitate the access of substrates to the enzyme active site. Moreover, steered molecular dynamics docking simulations have shown that lignin peroxidase natural substrate (veratryl alcohol) can easily approach the heme edge through the access channel. PMID:12770894
Dynamic combinatorial libraries: from exploring molecular recognition to systems chemistry.
Li, Jianwei; Nowak, Piotr; Otto, Sijbren
2013-06-26
Dynamic combinatorial chemistry (DCC) is a subset of combinatorial chemistry where the library members interconvert continuously by exchanging building blocks with each other. Dynamic combinatorial libraries (DCLs) are powerful tools for discovering the unexpected and have given rise to many fascinating molecules, ranging from interlocked structures to self-replicators. Furthermore, dynamic combinatorial molecular networks can produce emergent properties at systems level, which provide exciting new opportunities in systems chemistry. In this perspective we will highlight some new methodologies in this field and analyze selected examples of DCLs that are under thermodynamic control, leading to synthetic receptors, catalytic systems, and complex self-assembled supramolecular architectures. Also reviewed are extensions of the principles of DCC to systems that are not at equilibrium and may therefore harbor richer functional behavior. Examples include self-replication and molecular machines.
Karp, Jerome M.; Erylimaz, Ertan
2015-01-01
There has been a longstanding interest in being able to accurately predict NMR chemical shifts from structural data. Recent studies have focused on using molecular dynamics (MD) simulation data as input for improved prediction. Here we examine the accuracy of chemical shift prediction for intein systems, which have regions of intrinsic disorder. We find that using MD simulation data as input for chemical shift prediction does not consistently improve prediction accuracy over use of a static X-ray crystal structure. This appears to result from the complex conformational ensemble of the disordered protein segments. We show that using accelerated molecular dynamics (aMD) simulations improves chemical shift prediction, suggesting that methods which better sample the conformational ensemble like aMD are more appropriate tools for use in chemical shift prediction for proteins with disordered regions. Moreover, our study suggests that data accurately reflecting protein dynamics must be used as input for chemical shift prediction in order to correctly predict chemical shifts in systems with disorder. PMID:25416617
TOPICAL REVIEW: Ab initio molecular dynamics: basic concepts, current trends and novel applications
NASA Astrophysics Data System (ADS)
Tuckerman, Mark E.
2002-12-01
The field of ab initio molecular dynamics (AIMD), in which finite temperature molecular dynamics (MD) trajectories are generated with forces obtained from accurate 'on the fly' electronic structure calculations, is a rapidly evolving and growing technology that allows chemical processes in condensed phases to be studied in an accurate and unbiased way. This article is intended to present the basics of the AIMD method as well as to provide a broad survey of the state of the art of the field and showcase some of its capabilities. Beginning with a derivation of the method from the Born-Oppenheimer approximation, issues including the density functional representation of electronic structure, basis sets, calculation of observables and the Car-Parrinello extended Lagrangian algorithm are discussed. A number of example applications, including liquid structure and dynamics and aqueous proton transport, are presented in order to highlight some of the current capabilities of the approach. Finally, advanced topics such as inclusion of nuclear quantum effects, excited states and scaling issues are addressed.
Davidchack, Ruslan L.
2010-12-10
We investigate the influence of numerical discretization errors on computed averages in a molecular dynamics simulation of TIP4P liquid water at 300 K coupled to different deterministic (Nose-Hoover and Nose-Poincare) and stochastic (Langevin) thermostats. We propose a couple of simple practical approaches to estimating such errors and taking them into account when computing the averages. We show that it is possible to obtain accurate measurements of various system quantities using step sizes of up to 70% of the stability threshold of the integrator, which for the system of TIP4P liquid water at 300 K corresponds to the step size of about 7 fs.
NASA Astrophysics Data System (ADS)
Cortes-Huerto, R.; Kremer, K.; Potestio, R.
2016-10-01
We present an accurate and efficient method to obtain Kirkwood-Buff (KB) integrals in the thermodynamic limit from small-sized molecular dynamics simulations. By introducing finite size effects into integral equations of statistical mechanics, we derive an analytical expression connecting the KB integrals of the bulk system with the fluctuations of the number of molecules in the corresponding closed system. We validate the method by calculating the activity coefficients of aqueous urea mixtures and the KB integrals of Lennard-Jones fluids. Moreover, our results demonstrate how to identify simulation conditions under which computer simulations reach the thermodynamic limit.
Guan, Tao; Zhou, Dongxiang; Liu, Yunhui
2015-07-01
Overlapping cells segmentation is one of the challenging topics in medical image processing. In this paper, we propose to approximately represent the cell contour as a set of sparse contour points, which can be further partitioned into two parts: the strong contour points and the weak contour points. We consider the cell contour extraction as a contour points locating problem and propose an effective and robust framework for segmentation of partially overlapping cells in cervical smear images. First, the cell nucleus and the background are extracted by a morphological filtering-based K-means clustering algorithm. Second, a gradient decomposition-based edge enhancement method is developed for enhancing the true edges belonging to the center cell. Then, a dynamic sparse contour searching algorithm is proposed to gradually locate the weak contour points in the cell overlapping regions based on the strong contour points. This algorithm involves the least squares estimation and a dynamic searching principle, and is thus effective to cope with the cell overlapping problem. Using the located contour points, the Gradient Vector Flow Snake model is finally employed to extract the accurate cell contour. Experiments have been performed on two cervical smear image datasets containing both single cells and partially overlapping cells. The high accuracy of the cell contour extraction result validates the effectiveness of the proposed method.
GAS PHASE MOLECULAR DYNAMICS: HIGH-RESOLUTION SPECTROSCOPIC PROBES OF CHEMICAL DYNAMICS.
HALL, G.E.
2006-05-30
This research is carried out as part of the Gas Phase Molecular Dynamics group program in the Chemistry Department at Brookhaven National Laboratory. High-resolution spectroscopic tools are developed and applied to problems in chemical dynamics. Recent topics have included the state-resolved studies of collision-induced electronic energy transfer, dynamics of barrierless unimolecular reactions, and the kinetics and spectroscopy of transient species.
A random rotor molecule: Vibrational analysis and molecular dynamics simulations
NASA Astrophysics Data System (ADS)
Li, Yu; Zhang, Rui-Qin; Shi, Xing-Qiang; Lin, Zijing; Van Hove, Michel A.
2012-12-01
Molecular structures that permit intramolecular rotational motion have the potential to function as molecular rotors. We have employed density functional theory and vibrational frequency analysis to study the characteristic structure and vibrational behavior of the molecule (4',4″″-(bicyclo[2,2,2]octane-1,4-diyldi-4,1-phenylene)-bis-2,2':6',2″-terpyridine. IR active vibrational modes were found that favor intramolecular rotation. To demonstrate the rotor behavior of the isolated single molecule, ab initio molecular dynamics simulations at various temperatures were carried out. This molecular rotor is expected to be thermally triggered via excitation of specific vibrational modes, which implies randomness in its direction of rotation.
Laser-enhanced dynamics in molecular rate processes
NASA Technical Reports Server (NTRS)
George, T. F.; Zimmerman, I. H.; Devries, P. L.; Yuan, J.-M.; Lam, K.-S.; Bellum, J. C.; Lee, H.-W.; Slutsky, M. S.
1978-01-01
The present discussion deals with some theoretical aspects associated with the description of molecular rate processes in the presence of intense laser radiation, where the radiation actually interacts with the molecular dynamics. Whereas for weak and even moderately intense radiation, the absorption and stimulated emission of photons by a molecular system can be described by perturbative methods, for intense radiation, perturbation theory is usually not adequate. Limiting the analysis to the gas phase, an attempt is made to describe nonperturbative approaches applicable to the description of such processes (in the presence of intense laser radiation) as electronic energy transfer in molecular (in particular atom-atom) collisions; collision-induced ionization and emission; and unimolecular dissociation.
Molecular dynamics computer simulation of permeation in solids
Pohl, P.I.; Heffelfinger, G.S.; Fisler, D.K.; Ford, D.M.
1997-12-31
In this work the authors simulate permeation of gases and cations in solid models using molecular mechanics and a dual control volume grand canonical molecular dynamics technique. The molecular sieving nature of microporous zeolites are discussed and compared with that for amorphous silica made by sol-gel methods. One mesoporous and one microporous membrane model are tested with Lennard-Jones gases corresponding to He, H{sub 2}, Ar and CH{sub 4}. The mesoporous membrane model clearly follows a Knudsen diffusion mechanism, while the microporous model having a hard-sphere cutoff pore diameter of {approximately}3.4 {angstrom} demonstrates molecular sieving of the methane ({sigma} = 3.8 {angstrom}) but anomalous behavior for Ar ({sigma} = 3.4 {angstrom}). Preliminary results of Ca{sup +} diffusion in calcite and He/H{sub 2} diffusion in polyisobutylene are also presented.
Liu, Qixin; Cai, Zhiyong
2014-01-01
This paper presents studies on the characteristics of gas molecular mean free path in nanopores by molecular dynamics simulation. Our study results indicate that the mean free path of all molecules in nanopores depend on both the radius of the nanopore and the gas-solid interaction strength. Besides mean free path of all molecules in the nanopore, this paper highlights the gas molecular mean free path at different positions of the nanopore and the anisotropy of the gas molecular mean free path at nanopores. The molecular mean free path varies with the molecule’s distance from the center of the nanopore. The least value of the mean free path occurs at the wall surface of the nanopore. The present paper found that the gas molecular mean free path is anisotropic when gas is confined in nanopores. The radial gas molecular mean free path is much smaller than the mean free path including all molecular collisions occuring in three directions. Our study results also indicate that when gas is confined in nanopores the gas molecule number density does not affect the gas molecular mean free path in the same way as it does for the gas in unbounded space. These study results may bring new insights into understanding the gas flow’s characteristic at nanoscale. PMID:25046745
Molecular dynamics simulation: A tool for exploration and discovery
NASA Astrophysics Data System (ADS)
Rapaport, Dennis C.
2009-03-01
The exploratory and didactic aspects of science both benefit from the ever-growing role played by computer simulation. One particularly important simulational approach is the molecular dynamics method, used for studying the nature of matter from the molecular to much larger scales. The effectiveness of molecular dynamics can be enhanced considerably by employing visualization and interactivity during the course of the computation and afterwards, allowing the modeler not only to observe the detailed behavior of the systems simulated in different ways, but also to steer the computations in alternative directions by manipulating parameters that govern the actual behavior. This facilitates the creation of potentially rich simulational environments for examining a multitude of complex phenomena, as well as offering an opportunity for enriching the learning process. A series of relatively advanced examples involving molecular dynamics will be used to demonstrate the value of this approach, in particular, atomistic simulations of spontaneously emergent structured fluid flows (the classic Rayleigh--B'enard and Taylor--Couette problems), supramolecular self-assembly of highly symmetric shell structures (involved in the formation of viral capsids), and that most counterintuitive of phenomena, granular segregation (e.g., axial and radial separation in a rotating cylinder).
CO2 diffusion in champagne wines: a molecular dynamics study.
Perret, Alexandre; Bonhommeau, David A; Liger-Belair, Gérard; Cours, Thibaud; Alijah, Alexander
2014-02-20
Although diffusion is considered as the main physical process responsible for the nucleation and growth of carbon dioxide bubbles in sparkling beverages, the role of each type of molecule in the diffusion process remains unclear. In the present study, we have used the TIP5P and SPC/E water models to perform force field molecular dynamics simulations of CO2 molecules in water and in a water/ethanol mixture respecting Champagne wine proportions. CO2 diffusion coefficients were computed by applying the generalized Fick's law for the determination of multicomponent diffusion coefficients, a law that simplifies to the standard Fick's law in the case of champagnes. The CO2 diffusion coefficients obtained in pure water and water/ethanol mixtures composed of TIP5P water molecules were always found to exceed the coefficients obtained in mixtures composed of SPC/E water molecules, a trend that was attributed to a larger propensity of SPC/E water molecules to form hydrogen bonds. Despite the fact that the SPC/E model is more accurate than the TIP5P model to compute water self-diffusion and CO2 diffusion in pure water, the diffusion coefficients of CO2 molecules in the water/ethanol mixture are in much better agreement with the experimental values of 1.4 - 1.5 × 10(-9) m(2)/s obtained for Champagne wines when the TIP5P model is employed. This difference was deemed to rely on the larger propensity of SPC/E water molecules to maintain the hydrogen-bonded network between water molecules and form new hydrogen bonds with ethanol, although statistical issues cannot be completely excluded. The remarkable agreement between the theoretical CO2 diffusion coefficients obtained within the TIP5P water/ethanol mixture and the experimental data specific to Champagne wines makes us infer that the diffusion coefficient in these emblematic hydroalcoholic sparkling beverages is expected to remain roughly constant whathever their proportions in sugars, glycerol, or peptides.
A molecular dynamics study of polymer/graphene interfacial systems
Rissanou, Anastassia N.; Harmandaris, Vagelis
2014-05-15
Graphene based polymer nanocomposites are hybrid materials with a very broad range of technological applications. In this work, we study three hybrid polymer/graphene interfacial systems (polystyrene/graphene, poly(methyl methacrylate)/graphene and polyethylene/graphene) through detailed atomistic molecular dynamics (MD) simulations. Density profiles, structural characteristics and mobility aspects are being examined at the molecular level for all model systems. In addition, we compare the properties of the hybrid systems to the properties of the corresponding bulk ones, as well as to theoretical predictions.
Improving structure-based function prediction using molecular dynamics
Glazer, Dariya S.; Radmer, Randall J.; Altman, Russ B.
2009-01-01
Summary The number of molecules with solved three-dimensional structure but unknown function is increasing rapidly. Particularly problematic are novel folds with little detectable similarity to molecules of known function. Experimental assays can determine the functions of such molecules, but are time-consuming and expensive. Computational approaches can identify potential functional sites; however, these approaches generally rely on single static structures and do not use information about dynamics. In fact, structural dynamics can enhance function prediction: we coupled molecular dynamics simulations with structure-based function prediction algorithms that identify Ca2+ binding sites. When applied to 11 challenging proteins, both methods showed substantial improvement in performance, revealing 22 more sites in one case and 12 more in the other, with a modest increase in apparent false positives. Thus, we show that treating molecules as dynamic entities improves the performance of structure-based function prediction methods. PMID:19604472
Chemical Dynamics, Molecular Energetics, and Kinetics at the Synchrotron
Leone, Stephen R.; Ahmed, Musahid; Wilson, Kevin R.
2010-03-14
Scientists at the Chemical Dynamics Beamline of the Advanced Light Source in Berkeley are continuously reinventing synchrotron investigations of physical chemistry and chemical physics with vacuum ultraviolet light. One of the unique aspects of a synchrotron for chemical physics research is the widely tunable vacuum ultraviolet light that permits threshold ionization of large molecules with minimal fragmentation. This provides novel opportunities to assess molecular energetics and reaction mechanisms, even beyond simple gas phase molecules. In this perspective, significant new directions utilizing the capabilities at the Chemical Dynamics Beamline are presented, along with an outlook for future synchrotron and free electron laser science in chemical dynamics. Among the established and emerging fields of investigations are cluster and biological molecule spectroscopy and structure, combustion flame chemistry mechanisms, radical kinetics and product isomer dynamics, aerosol heterogeneous chemistry, planetary and interstellar chemistry, and secondary neutral ion-beam desorption imaging of biological matter and materials chemistry.
Accelerating ring-polymer molecular dynamics with parallel-replica dynamics
NASA Astrophysics Data System (ADS)
Lu, Chun-Yaung; Perez, Danny; Voter, Arthur F.
2016-06-01
Nuclear quantum effects are important for systems containing light elements, and the effects are more prominent in the low temperature regime where the dynamics also becomes sluggish. We show that parallel replica (ParRep) dynamics, an accelerated molecular dynamics approach for infrequent-event systems, can be effectively combined with ring-polymer molecular dynamics, a semiclassical trajectory approach that gives a good approximation to zero-point and tunneling effects in activated escape processes. The resulting RP-ParRep method is a powerful tool for reaching long time scales in complex infrequent-event systems where quantum dynamics are important. Two illustrative examples, symmetric Eckart barrier crossing and interstitial helium diffusion in Fe and Fe-Cr alloy, are presented to demonstrate the accuracy and long-time scale capability of this approach.
Accelerating ring-polymer molecular dynamics with parallel-replica dynamics.
Lu, Chun-Yaung; Perez, Danny; Voter, Arthur F
2016-06-28
Nuclear quantum effects are important for systems containing light elements, and the effects are more prominent in the low temperature regime where the dynamics also becomes sluggish. We show that parallel replica (ParRep) dynamics, an accelerated molecular dynamics approach for infrequent-event systems, can be effectively combined with ring-polymer molecular dynamics, a semiclassical trajectory approach that gives a good approximation to zero-point and tunneling effects in activated escape processes. The resulting RP-ParRep method is a powerful tool for reaching long time scales in complex infrequent-event systems where quantum dynamics are important. Two illustrative examples, symmetric Eckart barrier crossing and interstitial helium diffusion in Fe and Fe-Cr alloy, are presented to demonstrate the accuracy and long-time scale capability of this approach. PMID:27369499
ERIC Educational Resources Information Center
Elmore, Donald E.; Guayasamin, Ryann C.; Kieffer, Madeleine E.
2010-01-01
As computational modeling plays an increasingly central role in biochemical research, it is important to provide students with exposure to common modeling methods in their undergraduate curriculum. This article describes a series of computer labs designed to introduce undergraduate students to energy minimization, molecular dynamics simulations,…
Calculation of transport properties of liquid metals and their alloys via molecular dynamics
NASA Astrophysics Data System (ADS)
Cherne, Frank Joseph, III
The advanced casting modeler requires accurate viscosity and diffusivity data of liquid metals and their alloys. The present work discusses the use of equilibrium and non-equilibrium molecular dynamics techniques to obtain such data without having to rely on oversimplified phenomenological expressions or difficult and expensive experiments. Utilizing the embedded atom method (EAM), the viscosities and diffusivities for a series of equilibrium and non-equilibrium molecular dynamics simulations of nickel, aluminum, and nickel-aluminum alloys are presented. A critical comparison between the equilibrium and non-equilibrium methods is presented. Besides the transport properties, structural data for the liquids are also evaluated. EAM does a poor job of describing the transport properties of nickel-aluminum alloys, particularly near the equiatomic concentration. It has been suggested that charge transfer between nickel and aluminum atoms is responsible for the discrepancy between numerical calculations and available experimental data. A modified electronic distribution function has been developed to simulate the charge transfer associated with compound formation. The effects of such a "charge transfer" modification to the embedded atom method are evaluated. The results of these simulations indicate that the embedded atom method combined with molecular dynamics may be used as a method to predict reasonably the transport properties.
Nakata, Hiroya; Schmidt, Michael W; Fedorov, Dmitri G; Kitaura, Kazuo; Nakamura, Shinichiro; Gordon, Mark S
2014-10-16
The fully analytic energy gradient has been developed and implemented for the restricted open-shell Hartree–Fock (ROHF) method based on the fragment molecular orbital (FMO) theory for systems that have multiple open-shell molecules. The accuracy of the analytic ROHF energy gradient is compared with the corresponding numerical gradient, illustrating the accuracy of the analytic gradient. The ROHF analytic gradient is used to perform molecular dynamics simulations of an unusual open-shell system, liquid oxygen, and mixtures of oxygen and nitrogen. These molecular dynamics simulations provide some insight about how triplet oxygen molecules interact with each other. Timings reveal that the method can calculate the energy gradient for a system containing 4000 atoms in only 6 h. Therefore, it is concluded that the FMO-ROHF method will be useful for investigating systems with multiple open shells.
Nakata, Hiroya; Schmidt, Michael W; Fedorov, Dmitri G; Kitaura, Kazuo; Nakamura, Shinichiro; Gordon, Mark S
2014-10-16
The fully analytic energy gradient has been developed and implemented for the restricted open-shell Hartree-Fock (ROHF) method based on the fragment molecular orbital (FMO) theory for systems that have multiple open-shell molecules. The accuracy of the analytic ROHF energy gradient is compared with the corresponding numerical gradient, illustrating the accuracy of the analytic gradient. The ROHF analytic gradient is used to perform molecular dynamics simulations of an unusual open-shell system, liquid oxygen, and mixtures of oxygen and nitrogen. These molecular dynamics simulations provide some insight about how triplet oxygen molecules interact with each other. Timings reveal that the method can calculate the energy gradient for a system containing 4000 atoms in only 6 h. Therefore, it is concluded that the FMO-ROHF method will be useful for investigating systems with multiple open shells.
Molecular dynamics insight to phase transition in n-alkanes with carbon nanofillers
Rastogi, Monisha; Vaish, Rahul
2015-05-15
The present work aims to investigate the phase transition, dispersion and diffusion behavior of nanocomposites of carbon nanotube (CNT) and straight chain alkanes. These materials are potential candidates for organic phase change materials(PCMs) and have attracted flurry of research recently. Accurate experimental evaluation of the mass, thermal and transport properties of such composites is both difficult as well as economically taxing. Additionally it is crucial to understand the factors that results in modification or enhancement of their characteristic at atomic or molecular level. Classical molecular dynamics approach has been extended to elucidate the same. Bulk atomistic models have been generated and subjected to rigorous multistage equilibration. To reaffirm the approach, both canonical and constant-temperature, constant- pressure ensembles were employed to simulate the models under consideration. Explicit determination of kinetic, potential, non-bond and total energy assisted in understanding the enhanced thermal and transport property of the nanocomposites from molecular point of view. Crucial parameters including mean square displacement and simulated self diffusion coefficient precisely define the balance of the thermodynamic and hydrodynamic interactions. Radial distribution function also reflected the density variation, strength and mobility of the nanocomposites. It is expected that CNT functionalization could improve the dispersion within n-alkane matrix. This would further ameliorate the mass and thermal properties of the composite. Additionally, the determined density was in good agreement with experimental data. Thus, molecular dynamics can be utilized as a high throughput technique for theoretical investigation of nanocomposites PCMs.
Molecular dynamics insight to phase transition in n-alkanes with carbon nanofillers
NASA Astrophysics Data System (ADS)
Rastogi, Monisha; Vaish, Rahul
2015-05-01
The present work aims to investigate the phase transition, dispersion and diffusion behavior of nanocomposites of carbon nanotube (CNT) and straight chain alkanes. These materials are potential candidates for organic phase change materials(PCMs) and have attracted flurry of research recently. Accurate experimental evaluation of the mass, thermal and transport properties of such composites is both difficult as well as economically taxing. Additionally it is crucial to understand the factors that results in modification or enhancement of their characteristic at atomic or molecular level. Classical molecular dynamics approach has been extended to elucidate the same. Bulk atomistic models have been generated and subjected to rigorous multistage equilibration. To reaffirm the approach, both canonical and constant-temperature, constant- pressure ensembles were employed to simulate the models under consideration. Explicit determination of kinetic, potential, non-bond and total energy assisted in understanding the enhanced thermal and transport property of the nanocomposites from molecular point of view. Crucial parameters including mean square displacement and simulated self diffusion coefficient precisely define the balance of the thermodynamic and hydrodynamic interactions. Radial distribution function also reflected the density variation, strength and mobility of the nanocomposites. It is expected that CNT functionalization could improve the dispersion within n-alkane matrix. This would further ameliorate the mass and thermal properties of the composite. Additionally, the determined density was in good agreement with experimental data. Thus, molecular dynamics can be utilized as a high throughput technique for theoretical investigation of nanocomposites PCMs.
Molecular Dynamics Simulations of Laser Powered Carbon Nanotube Gears
NASA Technical Reports Server (NTRS)
Srivastava, Deepak; Globus, Al; Han, Jie; Chancellor, Marisa K. (Technical Monitor)
1997-01-01
Dynamics of laser powered carbon nanotube gears is investigated by molecular dynamics simulations with Brenner's hydrocarbon potential. We find that when the frequency of the laser electric field is much less than the intrinsic frequency of the carbon nanotube, the tube exhibits an oscillatory pendulam behavior. However, a unidirectional rotation of the gear with oscillating frequency is observed under conditions of resonance between the laser field and intrinsic gear frequencies. The operating conditions for stable rotations of the nanotube gears, powered by laser electric fields are explored, in these simulations.
Molecular dynamical simulations of melting behaviors of metal clusters
Hamid, Ilyar; Fang, Meng; Duan, Haiming
2015-04-15
The melting behaviors of metal clusters are studied in a wide range by molecular dynamics simulations. The calculated results show that there are fluctuations in the heat capacity curves of some metal clusters due to the strong structural competition; For the 13-, 55- and 147-atom clusters, variations of the melting points with atomic number are almost the same; It is found that for different metal clusters the dynamical stabilities of the octahedral structures can be inferred in general by a criterion proposed earlier by F. Baletto et al. [J. Chem. Phys. 116 3856 (2002)] for the statically stable structures.
Finite Temperature Quasicontinuum: Molecular Dynamics without all the Atoms
Dupuy, L; Tadmor, E B; Miller, R E; Phillips, R
2005-02-02
Using a combination of statistical mechanics and finite-element interpolation, the authors develop a coarse-grained (CG) alternative to molecular dynamics (MD) for crystalline solids at constant temperature. The new approach is significantly more efficient than MD and generalizes earlier work on the quasi-continuum method. The method is validated by recovering equilibrium properties of single crystal Ni as a function of temperature. CG dynamical simulations of nanoindentation reveal a strong dependence on temperature of the critical stress to nucleate dislocations under the indenter.
Application of two dimensional periodic molecular dynamics to interfaces.
NASA Astrophysics Data System (ADS)
Gay, David H.; Slater, Ben; Catlow, C. Richard A.
1997-08-01
We have applied two-dimensional molecular dynamics to the surface of a crystalline aspartame and the interface between the crystal face and a solvent (water). This has allowed us to look at the dynamic processes at the surface. Understanding the surface structure and properties are important to controlling the crystal morphology. The thermodynamic ensemble was constant Number, surface Area and Temperature (NAT). The calculations have been carried out using a 2D Ewald summation and 2D periodic boundary conditions for the short range potentials. The equations of motion integration has been carried out using the standard velocity Verlet algorithm.
Abeyrathne, Chathurika D; Halgamuge, Malka N; Farrell, Peter M; Skafidas, Efstratios
2014-07-21
We analyzed the dielectric properties of molecular liquids using the external field method with reaction field approximations. The applicability of this method to determine the dielectric properties of molecules with zero (1,4-dioxane) and non-zero (water and bio-molecular aqueous solutions) permanent dipole moment was studied. The relative static dielectric constant obtained using the external field method for polar and non-polar molecular liquids, including molecules with zero permanent dipole moment, agreed well with the experimental values presented in the literature. Our results indicate that the Debye relaxation time constants estimated from the non-equilibrium simulations using the external field method were accurate for molecules whose permanent dipole moments were less than 12 D.
The effect of molecular dynamics sampling on the calculated observable gas-phase structures.
Tikhonov, Denis S; Otlyotov, Arseniy A; Rybkin, Vladimir V
2016-07-21
In this study, we compare the performance of various ab initio molecular dynamics (MD) sampling methods for the calculation of the observable vibrationally-averaged gas-phase structures of benzene, naphthalene and anthracene molecules. Nose-Hoover (NH), canonical and quantum generalized-Langevin-equation (GLE) thermostats as well as the a posteriori quantum correction to the classical trajectories have been tested and compared to the accurate path-integral molecular dynamics (PIMD), static anharmonic vibrational calculations as well as to the experimental gas electron diffraction data. Classical sampling methods neglecting quantum effects (NH and canonical GLE thermostats) dramatically underestimate vibrational amplitudes for the bonded atom pairs, both C-H and C-C, the resulting radial distribution functions exhibit nonphysically narrow peaks. This deficiency is almost completely removed by taking the quantum effects on the nuclei into account. The quantum GLE thermostat and a posteriori correction to the canonical GLE and NH thermostatted trajectories capture most vibrational quantum effects and closely reproduce computationally expensive PIMD and experimental radial distribution functions. These methods are both computationally feasible and accurate and are therefore recommended for calculations of the observable gas-phase structures. A good performance of the quantum GLE thermostat for the gas-phase calculations is encouraging since its parameters have been originally fitted for the condensed-phase calculations. Very accurate molecular structures can be predicted by combining the equilibrium geometry obtained at a high level of electronic structure theory with vibrational amplitudes and corrections calculated using MD driven by a lower level of electronic structure theory.
The effect of molecular dynamics sampling on the calculated observable gas-phase structures.
Tikhonov, Denis S; Otlyotov, Arseniy A; Rybkin, Vladimir V
2016-07-21
In this study, we compare the performance of various ab initio molecular dynamics (MD) sampling methods for the calculation of the observable vibrationally-averaged gas-phase structures of benzene, naphthalene and anthracene molecules. Nose-Hoover (NH), canonical and quantum generalized-Langevin-equation (GLE) thermostats as well as the a posteriori quantum correction to the classical trajectories have been tested and compared to the accurate path-integral molecular dynamics (PIMD), static anharmonic vibrational calculations as well as to the experimental gas electron diffraction data. Classical sampling methods neglecting quantum effects (NH and canonical GLE thermostats) dramatically underestimate vibrational amplitudes for the bonded atom pairs, both C-H and C-C, the resulting radial distribution functions exhibit nonphysically narrow peaks. This deficiency is almost completely removed by taking the quantum effects on the nuclei into account. The quantum GLE thermostat and a posteriori correction to the canonical GLE and NH thermostatted trajectories capture most vibrational quantum effects and closely reproduce computationally expensive PIMD and experimental radial distribution functions. These methods are both computationally feasible and accurate and are therefore recommended for calculations of the observable gas-phase structures. A good performance of the quantum GLE thermostat for the gas-phase calculations is encouraging since its parameters have been originally fitted for the condensed-phase calculations. Very accurate molecular structures can be predicted by combining the equilibrium geometry obtained at a high level of electronic structure theory with vibrational amplitudes and corrections calculated using MD driven by a lower level of electronic structure theory. PMID:27331660
Visual verification and analysis of cluster detection for molecular dynamics.
Grottel, Sebastian; Reina, Guido; Vrabec, Jadran; Ertl, Thomas
2007-01-01
A current research topic in molecular thermodynamics is the condensation of vapor to liquid and the investigation of this process at the molecular level. Condensation is found in many physical phenomena, e.g. the formation of atmospheric clouds or the processes inside steam turbines, where a detailed knowledge of the dynamics of condensation processes will help to optimize energy efficiency and avoid problems with droplets of macroscopic size. The key properties of these processes are the nucleation rate and the critical cluster size. For the calculation of these properties it is essential to make use of a meaningful definition of molecular clusters, which currently is a not completely resolved issue. In this paper a framework capable of interactively visualizing molecular datasets of such nucleation simulations is presented, with an emphasis on the detected molecular clusters. To check the quality of the results of the cluster detection, our framework introduces the concept of flow groups to highlight potential cluster evolution over time which is not detected by the employed algorithm. To confirm the findings of the visual analysis, we coupled the rendering view with a schematic view of the clusters' evolution. This allows to rapidly assess the quality of the molecular cluster detection algorithm and to identify locations in the simulation data in space as well as in time where the cluster detection fails. Thus, thermodynamics researchers can eliminate weaknesses in their cluster detection algorithms. Several examples for the effective and efficient usage of our tool are presented. PMID:17968118
Visual verification and analysis of cluster detection for molecular dynamics.
Grottel, Sebastian; Reina, Guido; Vrabec, Jadran; Ertl, Thomas
2007-01-01
A current research topic in molecular thermodynamics is the condensation of vapor to liquid and the investigation of this process at the molecular level. Condensation is found in many physical phenomena, e.g. the formation of atmospheric clouds or the processes inside steam turbines, where a detailed knowledge of the dynamics of condensation processes will help to optimize energy efficiency and avoid problems with droplets of macroscopic size. The key properties of these processes are the nucleation rate and the critical cluster size. For the calculation of these properties it is essential to make use of a meaningful definition of molecular clusters, which currently is a not completely resolved issue. In this paper a framework capable of interactively visualizing molecular datasets of such nucleation simulations is presented, with an emphasis on the detected molecular clusters. To check the quality of the results of the cluster detection, our framework introduces the concept of flow groups to highlight potential cluster evolution over time which is not detected by the employed algorithm. To confirm the findings of the visual analysis, we coupled the rendering view with a schematic view of the clusters' evolution. This allows to rapidly assess the quality of the molecular cluster detection algorithm and to identify locations in the simulation data in space as well as in time where the cluster detection fails. Thus, thermodynamics researchers can eliminate weaknesses in their cluster detection algorithms. Several examples for the effective and efficient usage of our tool are presented.
Molecular Dynamics and Electron Density Studies of Siderophores and Peptides.
NASA Astrophysics Data System (ADS)
Fidelis, Krzysztof Andrzej
1990-08-01
The dissertation comprises three separate studies of siderophores and peptides. In the first of these studies the relative potential energies for a series of diastereomers of a siderophore neocoprogen I are evaluated with molecular mechanics force field methods. Charges on the hydroxamate moiety are determined with a synthetic model siderophore compound using valence population refinements, and alternatively, with the theoretical ab initio/ESP calculations. The single diastereomer found in the crystal structure is among four characterized by the low potential energy, while prevalence of Delta vs. Lambda configuration about the iron is found to be a property of the entire series. In the second study the crystal structure of a ferrichrome siderophore ferrirhodin is reported. The crystal structure conformation of the molecular backbone as well as the iron coordination geometry compare well with other ferrichrome structures. The differences between the acyl groups of ferrirubin and ferrirhodin are explored using the methods of molecular mechanics. The third study a 300 ps, 300 K, in vacuo molecular dynamics simulation of didemnin A and B yields distinct molecular conformers, which are different from the one found in the crystal structure or modeled in solution, using the Nuclear Overhauser Effect data. Evaluations of the relative potential energy are performed with short 10 ps simulations in solution. Didemnins are natural depsipeptides isolated from a Caribbean tunicate and characterized by particularly potent antiproliferative and immunomodulatory activity. Conformationally rigid and flexible regions of the molecule are described. A short review of the molecular mechanics methodology is given in the introduction.
Extrapolated gradientlike algorithms for molecular dynamics and celestial mechanics simulations.
Omelyan, I P
2006-09-01
A class of symplectic algorithms is introduced to integrate the equations of motion in many-body systems. The algorithms are derived on the basis of an advanced gradientlike decomposition approach. Its main advantage over the standard gradient scheme is the avoidance of time-consuming evaluations of force gradients by force extrapolation without any loss of precision. As a result, the efficiency of the integration improves significantly. The algorithms obtained are analyzed and optimized using an error-function theory. The best among them are tested in actual molecular dynamics and celestial mechanics simulations for comparison with well-known nongradient and gradient algorithms such as the Störmer-Verlet, Runge-Kutta, Cowell-Numerov, Forest-Ruth, Suzuki-Chin, and others. It is demonstrated that for moderate and high accuracy, the extrapolated algorithms should be considered as the most efficient for the integration of motion in molecular dynamics simulations. PMID:17025782
Annihilation of craters: Molecular dynamic simulations on a silver surface
Henriksson, K. O. E.; Nordlund, K.; Keinonen, J.
2007-12-15
The ability of silver cluster ions containing 13 atoms to fill in a preexisting crater with a radius of about 28 A ring on a silver (001) target has been investigated using molecular dynamics simulations and the molecular-dynamics-Monte Carlo corrected effective medium potential. The largest lateral distance r between crater and ion was about three times the radius of the preexisting crater, namely, 75 A ring . The results reveal that when r<20 A ring and r>60 A ring the preexisting crater is partially filled in, and for other distances there is a net growth of the crater. The lattice damage created by the cluster ions, the total sputtering yield, the cluster sputtering yield, and simulated transmission electron microscopy images of the irradiated targets are also presented.
Extrapolated gradientlike algorithms for molecular dynamics and celestial mechanics simulations.
Omelyan, I P
2006-09-01
A class of symplectic algorithms is introduced to integrate the equations of motion in many-body systems. The algorithms are derived on the basis of an advanced gradientlike decomposition approach. Its main advantage over the standard gradient scheme is the avoidance of time-consuming evaluations of force gradients by force extrapolation without any loss of precision. As a result, the efficiency of the integration improves significantly. The algorithms obtained are analyzed and optimized using an error-function theory. The best among them are tested in actual molecular dynamics and celestial mechanics simulations for comparison with well-known nongradient and gradient algorithms such as the Störmer-Verlet, Runge-Kutta, Cowell-Numerov, Forest-Ruth, Suzuki-Chin, and others. It is demonstrated that for moderate and high accuracy, the extrapolated algorithms should be considered as the most efficient for the integration of motion in molecular dynamics simulations.
Enhancing Protein Adsorption Simulations by Using Accelerated Molecular Dynamics
Mücksch, Christian; Urbassek, Herbert M.
2013-01-01
The atomistic modeling of protein adsorption on surfaces is hampered by the different time scales of the simulation ( s) and experiment (up to hours), and the accordingly different ‘final’ adsorption conformations. We provide evidence that the method of accelerated molecular dynamics is an efficient tool to obtain equilibrated adsorption states. As a model system we study the adsorption of the protein BMP-2 on graphite in an explicit salt water environment. We demonstrate that due to the considerably improved sampling of conformational space, accelerated molecular dynamics allows to observe the complete unfolding and spreading of the protein on the hydrophobic graphite surface. This result is in agreement with the general finding of protein denaturation upon contact with hydrophobic surfaces. PMID:23755156
Adiabatic molecular-dynamics-simulation-method studies of kinetic friction
NASA Astrophysics Data System (ADS)
Zhang, J.; Sokoloff, J. B.
2005-06-01
An adiabatic molecular-dynamics method is developed and used to study the Muser-Robbins model for dry friction (i.e., nonzero kinetic friction in the slow sliding speed limit). In this model, dry friction between two crystalline surfaces rotated with respect to each other is due to mobile molecules (i.e., dirt particles) adsorbed at the interface. Our adiabatic method allows us to quickly locate interface potential-well minima, which become unstable during sliding of the surfaces. Since dissipation due to friction in the slow sliding speed limit results from mobile molecules dropping out of such unstable wells, our method provides a way to calculate dry friction, which agrees extremely well with results found by conventional molecular dynamics for the same system, but our method is more than a factor of 10 faster.
Coherent Amplification of Ultrafast Molecular Dynamics in an Optical Oscillator.
Aharonovich, Igal; Pe'er, Avi
2016-02-19
Optical oscillators present a powerful optimization mechanism. The inherent competition for the gain resources between possible modes of oscillation entails the prevalence of the most efficient single mode. We harness this "ultrafast" coherent feedback to optimize an optical field in time, and show that, when an optical oscillator based on a molecular gain medium is synchronously pumped by ultrashort pulses, a temporally coherent multimode field can develop that optimally dumps a general, dynamically evolving vibrational wave packet, into a single vibrational target state. Measuring the emitted field opens a new window to visualization and control of fast molecular dynamics. The realization of such a coherent oscillator with hot alkali dimers appears within experimental reach.
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.
Molecular dynamics studies of U1A-RNA complexes.
Reyes, C M; Kollman, P A
1999-01-01
The U1A protein binds to a hairpin RNA and an internal-loop RNA with picomolar affinities. To probe the molecular basis of U1A binding, we performed state-of-the-art nanosecond molecular dynamics simulations on both complexes. The good agreement with experimental structures supports the protocols used in the simulations. We compare the dynamics, hydrogen-bonding occupancies, and interfacial flexibility of both complexes and also describe a rigid-body motion in the U1A-internal loop complex that is not observed in the U1A-hairpin simulation. We relate these observations to experimental mutational studies and highlight their significance in U1A binding affinity and specificity. PMID:10024175
Shock induced phase transition of water: Molecular dynamics investigation
NASA Astrophysics Data System (ADS)
Neogi, Anupam; Mitra, Nilanjan
2016-02-01
Molecular dynamics simulations were carried out using numerous force potentials to investigate the shock induced phenomenon of pure bulk liquid water. Partial phase transition was observed at single shock velocity of 4.0 km/s without requirement of any external nucleators. Change in thermodynamic variables along with radial distribution function plots and spectral analysis revealed for the first time in the literature, within the context of molecular dynamic simulations, the thermodynamic pathway leading to formation of ice VII from liquid water on shock loading. The study also revealed information for the first time in the literature about the statistical time-frame after passage of shock in which ice VII formation can be observed and variations in degree of crystallinity of the sample over the entire simulation time of 100 ns.
Molecular dynamic simulation of non-melt laser annealing process
NASA Astrophysics Data System (ADS)
Liren, Yan; Dai, Li; Wei, Zhang; Zhihong, Liu; Wei, Zhou; Quan, Wang
2016-03-01
Molecular dynamic simulation is performed to study the process of material annealing caused by a 266 nm pulsed laser. A micro-mechanism describing behaviors of silicon and impurity atoms during the laser annealing at a non-melt regime is proposed. After ion implantation, the surface of the Si wafer is acted by a high energy laser pulse, which loosens the material and partially frees both Si and impurity atoms. While the residual laser energy is absorbed by valence electrons, these atoms are recoiled and relocated to finally form a crystal. Energy-related movement behavior is observed by using the molecular dynamic method. The non-melt laser anneal appears to be quite sensitive to the energy density of the laser, as a small excess energy may causes a significant impurity diffusion. Such a result is also supported by our laser anneal experiment.
Long Timestep Molecular Dynamics on the Graphical Processing Unit
Sweet, James C.; Nowling, Ronald J.; Cickovski, Trevor; Sweet, Christopher R.; Pande, Vijay S.; Izaguirre, Jesús A.
2013-01-01
Molecular dynamics (MD) simulations now play a key role in many areas of theoretical chemistry, biology, physics, and materials science. In many cases, such calculations are significantly limited by the massive amount of computer time needed to perform calculations of interest. Herein, we present Long Timestep Molecular Dynamics (LTMD), a method to significantly speed MD simulations. In particular, we discuss new methods to calculate the needed terms in LTMD as well as issues germane to a GPU implementation. The resulting code, implemented in the OpenMM MD library, can achieve a significant 6-fold speed increase, leading to MD simulations on the order of 5 μs/day using implicit solvent models. PMID:24436689
Molecular dynamics modeling of a nanomaterials-water surface interaction
NASA Astrophysics Data System (ADS)
Nejat Pishkenari, Hossein; Keramati, Ramtin; Abdi, Ahmad; Minary-Jolandan, Majid
2016-04-01
In this article, we study the formation of nanomeniscus around a nanoneedle using molecular dynamics simulation approach. The results reveal three distinct phases in the time-evolution of meniscus before equilibrium according to the contact angle, meniscus height, and potential energy. In addition, we investigated the correlation between the nanoneedle diameter and nanomeniscus characteristics. The results have applications in various fields such as scanning probe microscopy and rheological measurements.
Quantum tunneling splittings from path-integral molecular dynamics
NASA Astrophysics Data System (ADS)
Mátyus, Edit; Wales, David J.; Althorpe, Stuart C.
2016-03-01
We illustrate how path-integral molecular dynamics can be used to calculate ground-state tunnelling splittings in molecules or clusters. The method obtains the splittings from ratios of density matrix elements between the degenerate wells connected by the tunnelling. We propose a simple thermodynamic integration scheme for evaluating these elements. Numerical tests on fully dimensional malonaldehyde yield tunnelling splittings in good overall agreement with the results of diffusion Monte Carlo calculations.
Smoothed-particle hydrodynamics and nonequilibrium molecular dynamics
Hoover, W. G.; Hoover, C. G.
1993-08-01
Gingold, Lucy, and Monaghan invented a grid-free version of continuum mechanics ``smoothed-particle hydrodynamics,`` in 1977. It is a likely contributor to ``hybrid`` simulations combining atomistic and continuum simulations. We describe applications of this particle-based continuum technique from the closely-related standpoint of nonequilibrium molecular dynamics. We compare chaotic Lyapunov spectra for atomistic solids and fluids with those which characterize a two-dimensional smoothed-particle fluid system.
Phase transitions of methane using molecular dynamics simulations
NASA Astrophysics Data System (ADS)
El-Sheikh, S. M.; Barakat, K.; Salem, N. M.
2006-03-01
Using a short ranged Lennard-Jones interaction and a long ranged electrostatic potential, CH4under high pressure was modeled. Molecular dynamics simulations on small clusters (108 and 256molecules) were used to explore the phase diagram. Regarding phase transitions at different temperatures, our numerical findings are consistent with experimental results to a great degree. In addition, the hysteresis effect is displayed in our results.
Phase transitions of methane using molecular dynamics simulations.
El-Sheikh, S M; Barakat, K; Salem, N M
2006-03-28
Using a short ranged Lennard-Jones interaction and a long ranged electrostatic potential, CH4 under high pressure was modeled. Molecular dynamics simulations on small clusters (108 and 256 molecules) were used to explore the phase diagram. Regarding phase transitions at different temperatures, our numerical findings are consistent with experimental results to a great degree. In addition, the hysteresis effect is displayed in our results.
Simulational nanoengineering: Molecular dynamics implementation of an atomistic Stirling engine.
Rapaport, D C
2009-04-01
A nanoscale-sized Stirling engine with an atomistic working fluid has been modeled using molecular dynamics simulation. The design includes heat exchangers based on thermostats, pistons attached to a flywheel under load, and a regenerator. Key aspects of the behavior, including the time-dependent flows, are described. The model is shown to be capable of stable operation while producing net work at a moderate level of efficiency.
Molecular dynamics simulations of ordering of polydimethylsiloxane under uniaxial extension
Lacevic, N M; Gee, R H
2005-03-11
Molecular dynamics simulations of a bulk melts of polydimethylsiloxane (PDMS) are utilized to study chain conformation and ordering under constant uniaxial tension. We find that large extensions induce chain ordering in the direction of applied tension. We also find that voids are created via a cavitation mechanism. This study represents a validation of the current model for PDMS and benchmark for the future study of mechanical properties of PDMS melts enriched with fillers under tension.
A molecular dynamics study on sI hydrogen hydrate.
Mondal, S; Ghosh, S; Chattaraj, P K
2013-07-01
A molecular dynamics simulation is carried out to explore the possibility of using sI clathrate hydrate as hydrogen storage material. Metastable hydrogen hydrate structures are generated using the LAMMPS software. Different binding energies and radial distribution functions provide important insights into the behavior of the various types of hydrogen and oxygen atoms present in the system. Clathrate hydrate cages become more stable in the presence of guest molecules like hydrogen.
Simulational nanoengineering: Molecular dynamics implementation of an atomistic Stirling engine.
Rapaport, D C
2009-04-01
A nanoscale-sized Stirling engine with an atomistic working fluid has been modeled using molecular dynamics simulation. The design includes heat exchangers based on thermostats, pistons attached to a flywheel under load, and a regenerator. Key aspects of the behavior, including the time-dependent flows, are described. The model is shown to be capable of stable operation while producing net work at a moderate level of efficiency. PMID:19518394
Molecular dynamics simulation of shocks in porous TATB crystals
Fried, L.E.; Tarver, C.
1995-08-01
We report molecular dynamics results on the shock structure of 2-D crystals of triaminotrinitrobenzene (TATB). We find that the shock front broadens to approx. 30 nm in materials with a 20% random void distribution. As expected from bulk experiments, the shock velocity decreases with increasing porosity and the temperature behind the shock front increases with increasing porosity. Shock equilibration times increase from 1 ps to greater than 10 ps.
Molecular Dynamics study of Pb overlayer on Cu(100)
NASA Technical Reports Server (NTRS)
Karimi, M.; Tibbits, P.; Ila, D.; Dalins, I.; Vidali, G.
1991-01-01
Isothermal-isobaric Molecular Dynamics (MD) simulation of a submonolayer Pb film in c(2x2) ordered structure adsorbed on a Cu(100) substrate showed retention of order to high T. The Embedded Atom Method (EAM) calculated the energy of atoms of overlayer and substrate. The time-averaged squared modulus of the two dimensional structure factor for the Pb overlayer measured the order of the overlayer. The results are for increasing T only, and require verification by simulated cooling.
Dynamically Arranging Gold Nanoparticles on DNA Origami for Molecular Logic Gates.
Yang, Jing; Song, Zhichao; Liu, Shi; Zhang, Qiang; Zhang, Cheng
2016-08-31
In molecular engineering, DNA molecules have been extensively studied owing to their capacity for accurate structural control and complex programmability. Recent studies have shown that the versatility and predictability of DNA origami make it an excellent platform for constructing nanodevices. In this study, we developed a strand-displacing strategy to selectively and dynamically release specific gold nanoparticles (AuNPs) on a rectangular DNA origami. A set of DNA logic gates ("OR", "AND", and "three-input majority gate") were established based on this strategy, in which computing results were identified by disassembly between the AuNPs and DNA origami. The computing results were detected using experimental approaches such as gel electrophoresis and transmission electron microscopy (TEM). This method can be used to assemble more complex nanosystems and may have potential applications for molecular engineering. PMID:27501932
Molecular dynamics simulations of solutions at constant chemical potential
NASA Astrophysics Data System (ADS)
Perego, C.; Salvalaglio, M.; Parrinello, M.
2015-04-01
Molecular dynamics studies of chemical processes in solution are of great value in a wide spectrum of applications, which range from nano-technology to pharmaceutical chemistry. However, these calculations are affected by severe finite-size effects, such as the solution being depleted as the chemical process proceeds, which influence the outcome of the simulations. To overcome these limitations, one must allow the system to exchange molecules with a macroscopic reservoir, thus sampling a grand-canonical ensemble. Despite the fact that different remedies have been proposed, this still represents a key challenge in molecular simulations. In the present work, we propose the Constant Chemical Potential Molecular Dynamics (CμMD) method, which introduces an external force that controls the environment of the chemical process of interest. This external force, drawing molecules from a finite reservoir, maintains the chemical potential constant in the region where the process takes place. We have applied the CμMD method to the paradigmatic case of urea crystallization in aqueous solution. As a result, we have been able to study crystal growth dynamics under constant supersaturation conditions and to extract growth rates and free-energy barriers.
Ultrafast Molecular Dynamics probed by Vacuum Ultraviolet Pulses
NASA Astrophysics Data System (ADS)
Cryan, James; Champenois, Elio; Shivaram, Niranjan; Wright, Travis; Yang, Chan-Shan; Falcone, Roger; Belkacem, Ali
2014-05-01
We present time-resolved measurements of the relaxation dynamics in small molecular systems (CO2 and C2H4) following ultraviolet (UV) photo-excitation. We probe these excitations through photoionization and velocity map imaging (VMI) spectroscopy. Vacuum and extreme ultraviolet (VUV/XUV) pump and probe pulses are created by exploiting strong-field high harmonic generation (HHG) from our state-of-the-art 30 mJ, 1 kHz laser system. Three dimensional photoelectron and photoion momentum images recorded with our VMI spectrometer reveal non-Born Oppenheimer dynamics in the vicinity of a conical intersection, and allow us track the state of the system as a function of time. We also present initial experiments with the goal of controlling the dynamics near a conical intersection using a strong-field IR pulse. Finally, we will show progress towards measurements of time-resolved molecular frame photoelectron angular distributions (TRMFPADs) by applying our VUV/XUV pulse sequence to an aligned molecular ensemble. Supported by Chemical Sciences, Geosciences and Biosciences division of BES/DOE.
Molecular-level dynamics of refractory dissolved organic matter
NASA Astrophysics Data System (ADS)
Niggemann, J.; Gerdts, G.; Dittmar, T.
2012-04-01
Refractory dissolved organic matter (DOM) accounts for most of the global oceanic organic carbon inventory. Processes leading to its formation and factors determining its stability are still largely unknown. We hypothesize that refractory DOM carries a universal molecular signature. Characterizing spatial and temporal variability in this universal signature is a key to understanding dynamics of refractory DOM. We present results from a long-term study of the DOM geo-metabolome in the open North Sea. Geo-metabolomics considers the entity of DOM as a population of compounds, each characterized by a specific function and reactivity in the cycling of energy and elements. Ten-thousands of molecular formulae were identified in DOM by ultrahigh resolution mass spectrometry analysis (FT-ICR-MS, Fourier-Transform Ion Cyclotron Resonance Mass Spectrometry). The DOM pool in the North Sea was influenced by a complex interplay of processes that produced, transformed and degraded dissolved molecules. We identified a stable fraction in North Sea DOM with a molecular composition similar to deep ocean DOM. Molecular-level changes in this stable fraction provide novel information on dynamics and interactions of refractory DOM.
Hall, G.E.
2011-05-31
This research is carried out as part of the Gas-Phase Molecular Dynamics program in the Chemistry Department at Brookhaven National Laboratory. Chemical intermediates in the elementary gas-phase reactions involved in combustion chemistry are investigated by high resolution spectroscopic tools. Production, reaction, and energy transfer processes are investigated by transient, double resonance, polarization and saturation spectroscopies, with an emphasis on technique development and connection with theory, as well as specific molecular properties.
Hall G. E.; Goncharov, V.
2012-05-29
This research is carried out as part of the Gas-Phase Molecular Dynamics program in the Chemistry Department at Brookhaven National Laboratory. Chemical intermediates in the elementary gas-phase reactions involved in combustion chemistry are investigated by high resolution spectroscopic tools. Production, reaction, and energy transfer processes are investigated by transient, double resonance, polarization and saturation spectroscopies, with an emphasis on technique development and connection with theory, as well as specific molecular properties.
NASA Astrophysics Data System (ADS)
Moradi, Mahmoud; Babin, Volodymyr; Roland, Christopher; Sagui, Celeste
2010-09-01
Folded polyproline peptides can exist as either left-(PPII) or right-handed (PPI) helices, depending on their environment. In this work, we have characterized the conformations and the free energy landscapes of Ace-(Pro)n-Nme, n =2,3,…,9, and 13 peptides both in vacuo and in an implicit solvent environment. In order to enhance the sampling provided by regular molecular dynamics simulations, we have used the recently developed adaptively biased molecular dynamics method—which provides an accurate description of the free energy landscapes in terms of a set of relevant collective variables—combined with Hamiltonian and temperature replica exchange molecular dynamics methods. The collective variables, which are chosen so as to reflect the stable structures and the "slow modes" of the polyproline system, were based primarily on properties of length and of the cis/trans isomerization associated with the prolyl bonds. Results indicate that the space of peptide structures is characterized not just by pure PPII and PPI structures, but rather by a broad distribution of stable minima with similar free energies. These results are in agreement with recent experimental work. In addition, we have used steered molecular dynamics methods in order to quantitatively estimate the free energy difference of PPI and PPII for peptides of the length n =2,…,5 in vacuo and implicit water and qualitatively investigate transition pathways and mechanisms for the PPII to PPI transitions. A zipper-like mechanism, starting from either the center of the peptide or the amidated end, appear to be the most likely mechanisms for the PPII→PPI transition for the longer peptides.
Yamamori, Yu; Kitao, Akio
2013-10-14
A new and efficient conformational sampling method, MuSTAR MD (Multi-scale Sampling using Temperature Accelerated and Replica exchange Molecular Dynamics), is proposed to calculate the free energy landscape on a space spanned by a set of collective variables. This method is an extension of temperature accelerated molecular dynamics and can also be considered as a variation of replica-exchange umbrella sampling. In the MuSTAR MD, each replica contains an all-atom fine-grained model, at least one coarse-grained model, and a model defined by the collective variables that interacts with the other models in the same replica through coupling energy terms. The coarse-grained model is introduced to drive efficient sampling of large conformational space and the fine-grained model can serve to conduct more accurate conformational sampling. The collective variable model serves not only to mediate the coarse- and fine-grained models, but also to enhance sampling efficiency by temperature acceleration. We have applied this method to Ala-dipeptide and examined the sampling efficiency of MuSTAR MD in the free energy landscape calculation compared to that for replica exchange molecular dynamics, replica exchange umbrella sampling, temperature accelerated molecular dynamics, and conventional MD. The results clearly indicate the advantage of sampling a relatively high energy conformational space, which is not sufficiently sampled with other methods. This feature is important in the investigation of transition pathways that go across energy barriers. MuSTAR MD was also applied to Met-enkephalin as a test case in which two Gō-like models were employed as the coarse-grained model.
Balliou, A.; Douvas, A. M.; Normand, P.; Argitis, P.; Glezos, N.; Tsikritzis, D.; Kennou, S.
2014-10-14
In this work we study the utilization of molecular transition metal oxides known as polyoxometalates (POMs), in particular the Keggin structure anions of the formula PW₁₂O₄₀³⁻, as active nodes for potential switching and/or fast writing memory applications. The active molecules are being integrated in hybrid Metal-Insulator/POM molecules-Semiconductor capacitors, which serve as prototypes allowing investigation of critical performance characteristics towards the design of more sophisticated devices. The charging ability as well as the electronic structure of the molecular layer is probed by means of electrical characterization, namely, capacitance-voltage and current-voltage measurements, as well as transient capacitance measurements, C (t), under step voltage polarization. It is argued that the transient current peaks observed are manifestations of dynamic carrier exchange between the gate electrode and specific molecular levels, while the transient C (t) curves under conditions of molecular charging can supply information for the rate of change of the charge that is being trapped and de-trapped within the molecular layer. Structural characterization via surface and cross sectional scanning electron microscopy as well as atomic force microscopy, spectroscopic ellipsometry, UV and Fourier-transform IR spectroscopies, UPS, and XPS contribute to the extraction of accurate electronic structure characteristics and open the path for the design of new devices with on-demand tuning of their interfacial properties via the controlled preparation of the POM layer.
Molecular Dynamics and Energy Minimization Based on Embedded Atom Method
1995-03-01
This program performs atomic scale computer simulations of the structure and dynamics of metallic system using energetices based on the Embedded Atom Method. The program performs two types of calculations. First, it performs local energy minimization of all atomic positions to determine ground state and saddle point energies and structures. Second, it performs molecular dynamics simulations to determine thermodynamics or miscroscopic dynamics of the system. In both cases, various constraints can be applied to themore » system. The volume of the system can be varied automatically to achieve any desired external pressure. The temperature in molecular dynamics simulations can be controlled by a variety of methods. Further, the temperature control can be applied either to the entire system or just a subset of the atoms that would act as a thermal source/sink. The motion of one or more of the atoms can be constrained to either simulate the effects of bulk boundary conditions or to facilitate the determination of saddle point configurations. The simulations are performed with periodic boundary conditions.« less
Prior, Javier; Castro, Enrique; Chin, Alex W.; Almeida, Javier; Huelga, Susana F.; Plenio, Martin B.
2013-12-14
New experimental techniques based on nonlinear ultrafast spectroscopies have been developed over the last few years, and have been demonstrated to provide powerful probes of quantum dynamics in different types of molecular aggregates, including both natural and artificial light harvesting complexes. Fourier transform-based spectroscopies have been particularly successful, yet “complete” spectral information normally necessitates the loss of all information on the temporal sequence of events in a signal. This information though is particularly important in transient or multi-stage processes, in which the spectral decomposition of the data evolves in time. By going through several examples of ultrafast quantum dynamics, we demonstrate that the use of wavelets provide an efficient and accurate way to simultaneously acquire both temporal and frequency information about a signal, and argue that this greatly aids the elucidation and interpretation of physical process responsible for non-stationary spectroscopic features, such as those encountered in coherent excitonic energy transport.
Molecular dynamics test of the Brownian description of Na(+) motion in water
NASA Technical Reports Server (NTRS)
Wilson, M. A.; Pohorille, A.; Pratt, L. R.
1985-01-01
The present paper provides the results of molecular dynamics calculations on a Na(+) ion in aqueous solution. Attention is given to the sodium-oxygen and sodium-hydrogen radial distribution functions, the velocity autocorrelation function for the Na(+) ion, the autocorrelation function of the force on the stationary ion, and the accuracy of Brownian motion assumptions which are basic to hydrodynamic models of ion dyanmics in solution. It is pointed out that the presented calculations provide accurate data for testing theories of ion dynamics in solution. The conducted tests show that it is feasible to calculate Brownian friction constants for ions in aqueous solutions. It is found that for Na(+) under the considered conditions the Brownian mobility is in error by only 60 percent.
Efficient molecular dynamics using geodesic integration and solvent–solute splitting
Leimkuhler, Benedict
2016-01-01
We present an approach to Langevin dynamics in the presence of holonomic constraints based on decomposition of the system into components representing geodesic flow, constrained impulse and constrained diffusion. We show that a particular ordering of the components results in an integrator that is an order of magnitude more accurate for configurational averages than existing alternatives. Moreover, by combining the geodesic integration method with a solvent–solute force splitting, we demonstrate that stepsizes of at least 8 fs can be used for solvated biomolecules with high sampling accuracy and without substantially altering diffusion rates, approximately increasing by a factor of two the efficiency of molecular dynamics sampling for such systems. The methods described in this article are easily implemented using the standard apparatus of modern simulation codes. PMID:27279779
Molecular dynamics simulations of lysozyme in water/sugar solutions
NASA Astrophysics Data System (ADS)
Lerbret, A.; Affouard, F.; Bordat, P.; Hédoux, A.; Guinet, Y.; Descamps, M.
2008-04-01
Structural and dynamical properties of the solvent at the protein/solvent interface have been investigated by molecular dynamics simulations of lysozyme in trehalose, maltose and sucrose solutions. Results are discussed in the framework of the bioprotection phenomena. The analysis of the relative concentration of water oxygen atoms around lysozyme suggests that lysozyme is preferentially hydrated. When comparing the three sugars, trehalose is seen more excluded than maltose and sucrose. The preferential exclusion of sugars from the protein surface induces some differences in the behavior of trehalose and maltose, particularly at 50 and 60 wt% concentrations, that are not observed experimentally in binary sugar/mixtures. The dynamical slowing down of the solvent is suggested to mainly arise from the homogeneity of the water/sugar matrices controlled by the percolation of the sugar hydrogen bonds networks. Furthermore, lysozyme strongly increases relaxation times of solvent molecules at the protein/solvent interface.
A rotary nano ion pump: a molecular dynamics study.
Lohrasebi, A; Feshanjerdi, M
2012-09-01
The dynamics of a rotary nano ion pump, inspired by the F (0) part of the F(0)F(1)-ATP synthase biomolecular motor, were investigated. This nanopump is composed of a rotor, which is constructed of two carbon nanotubes with benzene rings, and a stator, which is made of six graphene sheets. The molecular dynamics (MD) method was used to simulate the dynamics of the ion nanopump. When the rotor of the nanopump rotates mechanically, an ion gradient will be generated between the two sides of the nanopump. It is shown that the ion gradient generated by the nanopump is dependant on parameters such as the rotary frequency of the rotor, temperature and the amounts and locations of the positive and negative charges of the stator part of the nanopump. Also, an electrical potential difference is generated between the two sides of the pump as a result of its operation.
Molecular View on Supramolecular Chain and Association Dynamics
NASA Astrophysics Data System (ADS)
Monkenbusch, M.; Krutyeva, M.; Pyckhout-Hintzen, W.; Antonius, W.; Hövelmann, C. H.; Allgaier, J.; Brás, A.; Farago, B.; Wischnewski, A.; Richter, D.
2016-09-01
The chain and association dynamics of supramolecular polymer ensembles decisively determines their properties. Using neutron spin echo (NSE) spectroscopy we present molecular insight into the space and time evolution of this dynamics. Studying a well characterized ensemble of linearly associating telechelic poly(ethylene glycol) melts carrying triple H-bonding end groups, we show that H-bond breaking significantly impacts the mode spectrum of the associates. The breaking affects the mode contributions and not the relaxation times as was assumed previously. NSE spectra directly reveal the so far intangible H-bond lifetimes in the supramolecular melt and demonstrate that for both the microscopic and the macroscopic dynamics of the supramolecular ensemble the instantaneous average of the Mw distribution governs the system response at least as long as the Rouse picture applies.
The classical and quantum dynamics of molecular spins on graphene.
Cervetti, Christian; Rettori, Angelo; Pini, Maria Gloria; Cornia, Andrea; Repollés, Ana; Luis, Fernando; Dressel, Martin; Rauschenbach, Stephan; Kern, Klaus; Burghard, Marko; Bogani, Lapo
2016-02-01
Controlling the dynamics of spins on surfaces is pivotal to the design of spintronic and quantum computing devices. Proposed schemes involve the interaction of spins with graphene to enable surface-state spintronics and electrical spin manipulation. However, the influence of the graphene environment on the spin systems has yet to be unravelled. Here we explore the spin-graphene interaction by studying the classical and quantum dynamics of molecular magnets on graphene. Whereas the static spin response remains unaltered, the quantum spin dynamics and associated selection rules are profoundly modulated. The couplings to graphene phonons, to other spins, and to Dirac fermions are quantified using a newly developed model. Coupling to Dirac electrons introduces a dominant quantum relaxation channel that, by driving the spins over Villain's threshold, gives rise to fully coherent, resonant spin tunnelling. Our findings provide fundamental insight into the interaction between spins and graphene, establishing the basis for electrical spin manipulation in graphene nanodevices. PMID:26641019
(Artificial intelligence and molecular dynamics simulations of polymers)
Noid, D.W.
1990-08-27
The traveler participated in planning a new methodology for performing molecular dynamics simulation of polymers. Current computer polymer dynamics programs are either capable of very general calculations and are extremely inefficient or are very efficiently written for a particular computer architecture to study a specific polymer system. Both of these approaches involve tremendous efforts in FORTRAN programming. A combined effort of computer scientists and myself hope to develop an expert system to produce efficient FORTRAN codes for any polymer and be optimized on computer architectures ranging from TRANSPUTERS to CRAY. The result of this collaboration will be an efficient way to model polymer dynamics for an arbitrary polymer structure. The subsidiary purpose was to present a seminar at the University of Newcastle and discussions with several other departments at Oxford University.
Molecular dynamics studies of interfacial water at the alumina surface.
Argyris, Dr. Dimitrios; Ho, Thomas; Cole, David
2011-01-01
Interfacial water properties at the alumina surface were investigated via all-atom equilibrium molecular dynamics simulations at ambient temperature. Al-terminated and OH-terminated alumina surfaces were considered to assess the structural and dynamic behavior of the first few hydration layers in contact with the substrates. Density profiles suggest water layering up to {approx}10 {angstrom} from the solid substrate. Planar density distribution data indicate that water molecules in the first interfacial layer are organized in well-defined patterns dictated by the atomic terminations of the alumina surface. Interfacial water exhibits preferential orientation and delayed dynamics compared to bulk water. Water exhibits bulk-like behavior at distances greater than {approx}10 {angstrom} from the substrate. The formation of an extended hydrogen bond network within the first few hydration layers illustrates the significance of water?water interactions on the structural properties at the interface.
Acceleration of dynamic fluorescence molecular tomography with principal component analysis
Zhang, Guanglei; He, Wei; Pu, Huangsheng; Liu, Fei; Chen, Maomao; Bai, Jing; Luo, Jianwen
2015-01-01
Dynamic fluorescence molecular tomography (FMT) is an attractive imaging technique for three-dimensionally resolving the metabolic process of fluorescent biomarkers in small animal. When combined with compartmental modeling, dynamic FMT can be used to obtain parametric images which can provide quantitative pharmacokinetic information for drug development and metabolic research. However, the computational burden of dynamic FMT is extremely huge due to its large data sets arising from the long measurement process and the densely sampling device. In this work, we propose to accelerate the reconstruction process of dynamic FMT based on principal component analysis (PCA). Taking advantage of the compression property of PCA, the dimension of the sub weight matrix used for solving the inverse problem is reduced by retaining only a few principal components which can retain most of the effective information of the sub weight matrix. Therefore, the reconstruction process of dynamic FMT can be accelerated by solving the smaller scale inverse problem. Numerical simulation and mouse experiment are performed to validate the performance of the proposed method. Results show that the proposed method can greatly accelerate the reconstruction of parametric images in dynamic FMT almost without degradation in image quality. PMID:26114027
Confinement of conjugated polymers into soft nanoparticles: molecular dynamics simulations
NASA Astrophysics Data System (ADS)
Wijesinghe, Sidath; Perahia, Dvora; Grest, Gary S.
2013-03-01
The structure and dynamics of conjugated polymers confined into soft nanoparticles (SNPs) have been studies by molecular dynamic simulations. This new class of tunable luminescent SNPs exhibits an immense potential as bio-markers as well as targeted drug delivery agents where tethering specific groups to the surface particles offers a means to target specific applications. Of particular interest are SNPs that consist of non- crosslinked polymers, decorated with polar groups. These SNPs are potentially tunable through the dynamics of the polymer chains, whereas the polar entity serves as internal stabilizer and surface encore. Confinement of a polymer whose inherent conformation is extended impacts not only their dynamics and as a result their optical properties. Here we will present insight into the structure and dynamics of dialkyl poly para phenylene ethynylene (PPE), decorated by a carboxylate groups, confined into a soft particle. The conformation and dynamics of polymer within SNP will be discussed and compared with that of the linear chain in solution. This work in partially supported by DOE grant DE-FG02-12ER46843
NASA Astrophysics Data System (ADS)
Boek, E. S.; Jusufi, A.; Löwen, H.; Maitland, G. C.
2002-10-01
Understanding how macroscopic properties depend on intermolecular interactions for complex fluid systems is an enormous challenge in statistical mechanics. This issue is of particular importance for designing optimal industrial fluid formulations such as responsive oilfield fluids, based on viscoelastic surfactant solutions. We have carried out extensive molecular dynamics simulations, resolving the full chemical details in order to study how the structure of the lamellar phase of viscoelastic surfactant solutions depends on the head group (HG) chemistry of the surfactant. In particular, we consider anionic carboxylate and quaternary ammonium HGs with erucyl tails in aqueous solutions together with their sodium and chloride counterions at room temperature. We find a strong HG dependence of the lamellar structure as characterized by suitable pair correlation functions and density distributions. The depth of penetration of water into the bilayer membrane, the nature of counterion condensation on the HGs and even the order and correlation of the tails in the lamellae depend sensitively on the chemical details of the HG. We also determine the compressibility of the lamellar system as a first step to using atom-resolved molecular dynamics in order to link the molecular and macroscopic scales of length and time. The results give important insight into the links between molecular details and surfactant phase structure which is being exploited to develop more systematic procedures for the molecular design and formulation of industrial systems.
Hall,G.E.; Sears, T.J.
2009-04-03
This research is carried out as part of the Gas-Phase Molecular Dynamics program in the Chemistry Department at Brookhaven National Laboratory. High-resolution spectroscopy, augmented by theoretical and computational methods, is used to investigate the structure and collision dynamics of chemical intermediates in the elementary gas-phase reactions involved in combustion chemistry. Applications and methods development are equally important experimental components of this work.
Extended Molecular Dynamics Methods for Vortex Dynamics in Nano-structured Superconductors
NASA Astrophysics Data System (ADS)
Kato, Masaru; Sato, Osamu
Using improved molecular dynamics simulation method, we study vortex dynamics in nano-scaled superconductors. Heat generations during vortex motion, heat transfer in superconductors, and entropy forces to vortices are incorporated. Also quasi-particle relaxations after vortex motion, and their attractive "retarded" forces to other vortices are incorporated using the condensation-energy field. We show the time development of formation of vortex channel flow in a superconducting Corbino-disk.
Calcagno, Claudia; Lobatto, Mark E; Dyvorne, Hadrien; Robson, Philip M; Millon, Antoine; Senders, Max L; Lairez, Olivier; Ramachandran, Sarayu; Coolen, Bram F; Black, Alexandra; Mulder, Willem J M; Fayad, Zahi A
2015-10-01
Atherosclerotic plaques that cause stroke and myocardial infarction are characterized by increased microvascular permeability and inflammation. Dynamic contrast-enhanced MRI (DCE-MRI) has been proposed as a method to quantify vessel wall microvascular permeability in vivo. Until now, most DCE-MRI studies of atherosclerosis have been limited to two-dimensional (2D) multi-slice imaging. Although providing the high spatial resolution required to image the arterial vessel wall, these approaches do not allow the quantification of plaque permeability with extensive anatomical coverage, an essential feature when imaging heterogeneous diseases, such as atherosclerosis. To our knowledge, we present the first systematic evaluation of three-dimensional (3D), high-resolution, DCE-MRI for the extensive quantification of plaque permeability along an entire vascular bed, with validation in atherosclerotic rabbits. We compare two acquisitions: 3D turbo field echo (TFE) with motion-sensitized-driven equilibrium (MSDE) preparation and 3D turbo spin echo (TSE). We find 3D TFE DCE-MRI to be superior to 3D TSE DCE-MRI in terms of temporal stability metrics. Both sequences show good intra- and inter-observer reliability, and significant correlation with ex vivo permeability measurements by Evans Blue near-infrared fluorescence (NIRF). In addition, we explore the feasibility of using compressed sensing to accelerate 3D DCE-MRI of atherosclerosis, to improve its temporal resolution and therefore the accuracy of permeability quantification. Using retrospective under-sampling and reconstructions, we show that compressed sensing alone may allow the acceleration of 3D DCE-MRI by up to four-fold. We anticipate that the development of high-spatial-resolution 3D DCE-MRI with prospective compressed sensing acceleration may allow for the more accurate and extensive quantification of atherosclerotic plaque permeability along an entire vascular bed. We foresee that this approach may allow for
Self-Assembly and Dynamics of Organic 2D Molecular Sieves: Ab Initio and Molecular Dynamics Studies
NASA Astrophysics Data System (ADS)
St. John, Alexander; Wexler, Carlos
2015-03-01
Spontaneous molecular self-assembly is a promising route for bottom-up manufacturing of two-dimensional (2D) nanostructures with specific topologies on atomically flat surfaces. Of particular interest is the possibility of selective lock-and-key interaction of guest molecules inside cavities formed by complex self-assembled host structures. Our host structure is a monolayer consisting of interdigitated 1,3,5-tristyrylbenzene substituted by alkoxy peripheral chains containing n = 6, 8, 10, 12, or 14 carbon atoms (TSB3,5-C n) deposited on a highly ordered pyrolytic graphite (HOPG) surface. Using ab initio methods from quantum chemistry and molecular dynamics simulations, we construct and analyze the structure and functionality of the TSB3,5-C n monolayer as a molecular sieve. Supported by ACS-PRF 52696-ND5.
Decoration of gold nanoparticles with cysteine in solution: reactive molecular dynamics simulations
NASA Astrophysics Data System (ADS)
Monti, Susanna; Carravetta, Vincenzo; Ågren, Hans
2016-06-01
The dynamics of gold nanoparticle functionalization by means of adsorption of cysteine molecules in water solution is simulated through classical reactive molecular dynamics simulations based on an accurately parametrized force field. The adsorption modes of the molecules are characterized in detail disclosing the nature of the cysteine-gold interactions and the stability of the final material. The simulation results agree satisfactorily with recent experimental and theoretical data and confirm previous findings for a similar system. The covalent attachments of the molecules to the gold support are all slow physisorptions followed by fast chemisorptions. However, a great variety of binding arrangements can be observed. Interactions with the adsorbate caused surface modulations in terms of adatoms and dislocations which contributed to strengthen the cysteine adsorption.The dynamics of gold nanoparticle functionalization by means of adsorption of cysteine molecules in water solution is simulated through classical reactive molecular dynamics simulations based on an accurately parametrized force field. The adsorption modes of the molecules are characterized in detail disclosing the nature of the cysteine-gold interactions and the stability of the final material. The simulation results agree satisfactorily with recent experimental and theoretical data and confirm previous findings for a similar system. The covalent attachments of the molecules to the gold support are all slow physisorptions followed by fast chemisorptions. However, a great variety of binding arrangements can be observed. Interactions with the adsorbate caused surface modulations in terms of adatoms and dislocations which contributed to strengthen the cysteine adsorption. Electronic supplementary information (ESI) available: Different views of the AuNP surface coverage. Distance map describing the position of each molecule in relation to the others on the AuNP (alpha carbon distances). See DOI: 10.1039/C
Papaleo, Elena
2015-01-01
In the last years, we have been observing remarkable improvements in the field of protein dynamics. Indeed, we can now study protein dynamics in atomistic details over several timescales with a rich portfolio of experimental and computational techniques. On one side, this provides us with the possibility to validate simulation methods and physical models against a broad range of experimental observables. On the other side, it also allows a complementary and comprehensive view on protein structure and dynamics. What is needed now is a better understanding of the link between the dynamic properties that we observe and the functional properties of these important cellular machines. To make progresses in this direction, we need to improve the physical models used to describe proteins and solvent in molecular dynamics, as well as to strengthen the integration of experiments and simulations to overcome their own limitations. Moreover, now that we have the means to study protein dynamics in great details, we need new tools to understand the information embedded in the protein ensembles and in their dynamic signature. With this aim in mind, we should enrich the current tools for analysis of biomolecular simulations with attention to the effects that can be propagated over long distances and are often associated to important biological functions. In this context, approaches inspired by network analysis can make an important contribution to the analysis of molecular dynamics simulations. PMID:26075210
Papaleo, Elena
2015-01-01
In the last years, we have been observing remarkable improvements in the field of protein dynamics. Indeed, we can now study protein dynamics in atomistic details over several timescales with a rich portfolio of experimental and computational techniques. On one side, this provides us with the possibility to validate simulation methods and physical models against a broad range of experimental observables. On the other side, it also allows a complementary and comprehensive view on protein structure and dynamics. What is needed now is a better understanding of the link between the dynamic properties that we observe and the functional properties of these important cellular machines. To make progresses in this direction, we need to improve the physical models used to describe proteins and solvent in molecular dynamics, as well as to strengthen the integration of experiments and simulations to overcome their own limitations. Moreover, now that we have the means to study protein dynamics in great details, we need new tools to understand the information embedded in the protein ensembles and in their dynamic signature. With this aim in mind, we should enrich the current tools for analysis of biomolecular simulations with attention to the effects that can be propagated over long distances and are often associated to important biological functions. In this context, approaches inspired by network analysis can make an important contribution to the analysis of molecular dynamics simulations.
Accelerated molecular dynamics methods: introduction and recent developments
Uberuaga, Blas Pedro; Voter, Arthur F; Perez, Danny; Shim, Y; Amar, J G
2009-01-01
A long-standing limitation in the use of molecular dynamics (MD) simulation is that it can only be applied directly to processes that take place on very short timescales: nanoseconds if empirical potentials are employed, or picoseconds if we rely on electronic structure methods. Many processes of interest in chemistry, biochemistry, and materials science require study over microseconds and beyond, due either to the natural timescale for the evolution or to the duration of the experiment of interest. Ignoring the case of liquids xxx, the dynamics on these time scales is typically characterized by infrequent-event transitions, from state to state, usually involving an energy barrier. There is a long and venerable tradition in chemistry of using transition state theory (TST) [10, 19, 23] to directly compute rate constants for these kinds of activated processes. If needed dynamical corrections to the TST rate, and even quantum corrections, can be computed to achieve an accuracy suitable for the problem at hand. These rate constants then allow them to understand the system behavior on longer time scales than we can directly reach with MD. For complex systems with many reaction paths, the TST rates can be fed into a stochastic simulation procedure such as kinetic Monte Carlo xxx, and a direct simulation of the advance of the system through its possible states can be obtained in a probabilistically exact way. A problem that has become more evident in recent years, however, is that for many systems of interest there is a complexity that makes it difficult, if not impossible, to determine all the relevant reaction paths to which TST should be applied. This is a serious issue, as omitted transition pathways can have uncontrollable consequences on the simulated long-time kinetics. Over the last decade or so, we have been developing a new class of methods for treating the long-time dynamics in these complex, infrequent-event systems. Rather than trying to guess in advance what
Kanai, Y; Takeuchi, N
2009-10-14
We revisit the molecular line growth mechanism of styrene on the hydrogenated Si(001) 2x1 surface. In particular, we investigate the energetics of the radical chain reaction mechanism by means of diffusion quantum Monte Carlo (QMC) and density functional theory (DFT) calculations. For the exchange correlation (XC) functional we use the non-empirical generalized-gradient approximation (GGA) and meta-GGA. We find that the QMC result also predicts the intra dimer-row growth of the molecular line over the inter dimer-row growth, supporting the conclusion based on DFT results. However, the absolute magnitudes of the adsorption and reaction energies, and the heights of the energy barriers differ considerably between the QMC and DFT with the GGA/meta-GGA XC functionals.
Molecular dynamics modeling and characterization of graphene/polymer nanocomposites
NASA Astrophysics Data System (ADS)
Rahman, Rezwanur
The current work focuses on the characterization of graphene based nanocomposites using molecular dynamic simulation and multiscale modeling approaches. Both graphene-epoxy and graphene-cellulose nanocomposites were considered in this study. A hierarchical multiscale modeling approach has been proposed using peridynamics and molecular dynamics simulation. Firstly, the mechanical properties of crosslinked graphene/epoxy (G-Ep) nanocomposites were investigated by molecular mechanics (MM) and molecular dynamics (MD) simulations. The influence of graphene's weight concentration, aspect ratio and dispersion on stress-strain response and elastic properties were studied. The results show significant improvement in Young's modulus and shear modulus for the G-Ep system in comparison to the neat epoxy resin. It appears that the RDF, molecular energy and aspect ratios are influenced by both graphene concentrations and aspect ratios. The graphene concentrations in the range of 1-3% are seen to improve Young's modulus and shorter graphenes are observed to be more effective than larger ones. In addition, the dispersed graphene system is more promising in enhancing in-plane elastic modulus than the agglomerated graphene system. The cohesive and pullout forces versus displacements data were plotted under normal and shear modes in order to characterize interfacial properties. The cohesive force is significantly improved by attaching the graphene with a chemical bond at the graphene-epoxy interface. In the second part of the work, cellulose was considered to study the mechanical properties of graphene-cellulose bionanocomposite. Similar to graphene-epoxy systems, the effect of graphene dispersion and agglomeration were studied in the stress-strain plots of graphene-cellulose system. A pcff forcefield was used to define intermolecular and intramolecular interactions. The effect of graphene's aspect ratio and weight concentration on the structural property of each unitcell was
Molecular dynamics studies of protein folding and aggregation
NASA Astrophysics Data System (ADS)
Ding, Feng
This thesis applies molecular dynamics simulations and statistical mechanics to study: (i) protein folding; and (ii) protein aggregation. Most small proteins fold into their native states via a first-order-like phase transition with a major free energy barrier between the folded and unfolded states. A set of protein conformations corresponding to the free energy barrier, Delta G >> kBT, are the folding transition state ensemble (TSE). Due to their evasive nature, TSE conformations are hard to capture (probability ∝ exp(-DeltaG/k BT)) and characterize. A coarse-grained discrete molecular dynamics model with realistic steric constraints is constructed to reproduce the experimentally observed two-state folding thermodynamics. A kinetic approach is proposed to identify the folding TSE. A specific set of contacts, common to the TSE conformations, is identified as the folding nuclei which are necessary to be formed in order for the protein to fold. Interestingly, the amino acids at the site of the identified folding nuclei are highly conserved for homologous proteins sharing the same structures. Such conservation suggests that amino acids that are important for folding kinetics are under selective pressure to be preserved during the course of molecular evolution. In addition, studies of the conformations close to the transition states uncover the importance of topology in the construction of order parameter for protein folding transition. Misfolded proteins often form insoluble aggregates, amyloid fibrils, that deposit in the extracellular space and lead to a type of disease known as amyloidosis. Due to its insoluble and non-crystalline nature, the aggregation structure and, thus the aggregation mechanism, has yet to be uncovered. Discrete molecular dynamics studies reveal an aggregate structure with the same structural signatures as in experimental observations and show a nucleation aggregation scenario. The simulations also suggest a generic aggregation mechanism
Safaei, B; Naseradinmousavi, P; Rahmani, A
2016-04-01
In the present paper, an analytical solution based on a molecular mechanics model is developed to evaluate the elastic critical axial buckling strain of chiral multi-walled carbon nanotubes (MWCNTs). To this end, the total potential energy of the system is calculated with the consideration of the both bond stretching and bond angular variations. Density functional theory (DFT) in the form of generalized gradient approximation (GGA) is implemented to evaluate force constants used in the molecular mechanics model. After that, based on the principle of molecular mechanics, explicit expressions are proposed to obtain elastic surface Young's modulus and Poisson's ratio of the single-walled carbon nanotubes corresponding to different types of chirality. Selected numerical results are presented to indicate the influence of the type of chirality, tube diameter, and number of tube walls in detailed. An excellent agreement is found between the present numerical results and those found in the literature which confirms the validity as well as the accuracy of the present closed-form solution. It is found that the value of critical axial buckling strain exhibit significant dependency on the type of chirality and number of tube walls.
Computational Studies on the Anharmonic Dynamics of Molecular Clusters
NASA Astrophysics Data System (ADS)
Mancini, John S.
Molecular nanoclusters present ideal systems to probe the physical forces and dynamics that drive the behavior of larger bulk systems. At the nanocluster limit the first instances of several phenomena can be observed including the breaking of hydrogen and molecular bonds. Advancements in experimental and theoretical techniques have made it possible to explore these phenomena in great detail. The most fruitful of these studies have involved the use of both experimental and theoretical techniques to leverage to strengths of the two approaches. This dissertation seeks to explore several important phenomena of molecular clusters using new and existing theoretical methodologies. Three specific systems are considered, hydrogen chloride clusters, mixed water and hydrogen chloride clusters and the first cluster where hydrogen chloride autoionization occurs. The focus of these studies remain as close as possible to experimentally observable phenomena with the intention of validating, simulating and expanding on experimental work. Specifically, the properties of interested are those related to the vibrational ground and excited state dynamics of these systems. Studies are performed using full and reduced dimensional potential energy surface alongside advanced quantum mechanical methods including diffusion Monte Carlo, vibrational configuration interaction theory and quasi-classical molecular dynamics. The insight gained from these studies are great and varied. A new on-they-fly ab initio method for studying molecular clusters is validated for (HCl)1--6. A landmark study of the dissociation energy and predissociation mechanism of (HCl)3 is reported. The ground states of mixed (HCl)n(H2O)m are found to be highly delocalized across multiple stationary point configurations. Furthermore, it is identified that the consideration of this delocalization is required in vibrational excited state calculations to achieve agreement with experimental measurements. Finally, the theoretical
Study of critical dynamics in fluids via molecular dynamics in canonical ensemble.
Roy, Sutapa; Das, Subir K
2015-12-01
With the objective of understanding the usefulness of thermostats in the study of dynamic critical phenomena in fluids, we present results for transport properties in a binary Lennard-Jones fluid that exhibits liquid-liquid phase transition. Various collective transport properties, calculated from the molecular dynamics (MD) simulations in canonical ensemble, with different thermostats, are compared with those obtained from MD simulations in microcanonical ensemble. It is observed that the Nosé-Hoover and dissipative particle dynamics thermostats are useful for the calculations of mutual diffusivity and shear viscosity. The Nosé-Hoover thermostat, however, as opposed to the latter, appears inadequate for the study of bulk viscosity. PMID:26687057
Gas-Phase Molecular Dynamics: Theoretical Studies In Spectroscopy and Chemical Dynamics
Yu H. G.; Muckerman, J.T.
2012-05-29
The main goal of this program is the development and application of computational methods for studying chemical reaction dynamics and molecular spectroscopy in the gas phase. We are interested in developing rigorous quantum dynamics algorithms for small polyatomic systems and in implementing approximate approaches for complex ones. Particular focus is on the dynamics and kinetics of chemical reactions and on the rovibrational spectra of species involved in combustion processes. This research also explores the potential energy surfaces of these systems of interest using state-of-the-art quantum chemistry methods, and extends them to understand some important properties of materials in condensed phases and interstellar medium as well as in combustion environments.
Gas-Phase Molecular Dynamics: Theoretical Studies in Spectroscopy and Chemical Dynamics
Yu, H.G.; Muckerman, J.T.
2010-06-01
The goal of this program is the development and application of computational methods for studying chemical reaction dynamics and molecular spectroscopy in the gas phase. We are interested in developing rigorous quantum dynamics algorithms for small polyatomic systems and in implementing approximate approaches for complex ones. Particular focus is on the dynamics and kinetics of chemical reactions and on the rovibrational spectra of species involved in combustion processes. This research also explores the potential energy surfaces of these systems of interest using state-of-the-art quantum chemistry methods.
Dynamical Simulations of Molecular Clouds in the Galactic Center
NASA Astrophysics Data System (ADS)
Salas, Jesus; Morris, Mark
2016-06-01
The formation of the central massive cluster of young stars orbiting the Galactic black hole, Sgr A*, has been modeled by several groups by invoking an almost radially infalling molecular cloud that interacts with the black hole and creates a dense, gaseous disk in which stars can then form. However, the dynamical origin of such a cloud remains an open question. We present simulations of the central 30-100 pc of the Milky Way, starting from a population of molecular clouds located in a disk with scale height of ~30 pc, using the N-body/smoothed-particle hydrodynamics code, Gadget2. We followed the dynamical evolution of clouds in a galactic potential that includes a bar to explore whether cloud collisions or a succession of cloud scatterings can remove sufficient angular momentum from a massive cloud to endow it with a predominantly radial orbit. Initial results illustrate the importance of tidal shear; while dense cloud cores remain identifiable for extended periods of time, much of the molecular mass ends up in tidal streams, so cannot be deflected onto low angular momentum orbits by their mutual interactions. At the completion of our ongoing computations, we will report on whether the cloud cores can undergo sufficient scattering to achieve low-angular-momentum orbits.
Molecular Dynamics Simulation of Carbon Nanotube Based Gears
NASA Technical Reports Server (NTRS)
Han, Jie; Globus, Al; Jaffe, Richard; Deardorff, Glenn; Chancellor, Marisa K. (Technical Monitor)
1996-01-01
We used molecular dynamics to investigate the properties and design space of molecular gears fashioned from carbon nanotubes with teeth added via a benzyne reaction known to occur with C60. A modified, parallelized version of Brenner's potential was used to model interatomic forces within each molecule. A Leonard-Jones 6-12 potential was used for forces between molecules. One gear was powered by forcing the atoms near the end of the buckytube to rotate, and a second gear was allowed.to rotate by keeping the atoms near the end of its buckytube on a cylinder. The meshing aromatic gear teeth transfer angular momentum from the powered gear to the driven gear. A number of gear and gear/shaft configurations were simulated. Cases in vacuum and with an inert atmosphere were examined. In an extension to molecular dynamics technology, some simulations used a thermostat on the atmosphere while the hydrocarbon gear's temperature was allowed to fluctuate. This models cooling the gears with an atmosphere. Results suggest that these gears can operate at up to 50-100 gigahertz in a vacuum or inert atmosphere at room temperature. The failure mode involves tooth slip, not bond breaking, so failed gears can be returned to operation by lowering temperature and/or rotation rate. Videos and atomic trajectory files in xyz format are presented.
Recovering position-dependent diffusion from biased molecular dynamics simulations
Ljubetič, Ajasja; Urbančič, Iztok; Štrancar, Janez
2014-02-28
All atom molecular dynamics (MD) models provide valuable insight into the dynamics of biophysical systems, but are limited in size or length by the high computational demands. The latter can be reduced by simulating long term diffusive dynamics (also known as Langevin dynamics or Brownian motion) of the most interesting and important user-defined parts of the studied system, termed collective variables (colvars). A few hundred nanosecond-long biased MD trajectory can therefore be extended to millisecond lengths in the colvars subspace at a very small additional computational cost. In this work, we develop a method for determining multidimensional anisotropic position- and timescale-dependent diffusion coefficients (D) by analysing the changes of colvars in an existing MD trajectory. As a test case, we obtained D for dihedral angles of the alanine dipeptide. An open source Mathematica{sup ®} package, capable of determining and visualizing D in one or two dimensions, is available at https://github.com/lbf-ijs/DiffusiveDynamics . Given known free energy and D, the package can also generate diffusive trajectories.
Autoinhibitory mechanisms of ERG studied by molecular dynamics simulations
NASA Astrophysics Data System (ADS)
Lu, Yan; Salsbury, Freddie R.
2015-01-01
ERG, an ETS-family transcription factor, acts as a regulator of differentiation of early hematopoietic cells. It contains an autoinhibitory domain, which negatively regulates DNA-binding. The mechanism of autoinhibitory is still illusive. To understand the mechanism, we study the dynamical properties of ERG protein by molecular dynamics simulations. These simulations suggest that DNA binding autoinhibition associates with the internal dynamics of ERG. Specifically, we find that (1), The N-C terminal correlation in the inhibited ERG is larger than that in uninhibited ERG that contributes to the autoinhibition of DNA-binding. (2), DNA-binding changes the property of the N-C terminal correlation from being anti-correlated to correlated, that is, changing the relative direction of the correlated motions and (3), For the Ets-domain specifically, the inhibited and uninhibited forms exhibit essentially the same dynamics, but the binding of the DNA decreases the fluctuation of the Ets-domain. We also find from PCA analysis that the three systems, even with quite different dynamics, do have highly similar free energy surfaces, indicating that they share similar conformations.
Non-adiabatic molecular dynamics by accelerated semiclassical Monte Carlo
White, Alexander J.; Gorshkov, Vyacheslav N.; Tretiak, Sergei; Mozyrsky, Dmitry
2015-07-07
Non-adiabatic dynamics, where systems non-radiatively transition between electronic states, plays a crucial role in many photo-physical processes, such as fluorescence, phosphorescence, and photoisomerization. Methods for the simulation of non-adiabatic dynamics are typically either numerically impractical, highly complex, or based on approximations which can result in failure for even simple systems. Recently, the Semiclassical Monte Carlo (SCMC) approach was developed in an attempt to combine the accuracy of rigorous semiclassical methods with the efficiency and simplicity of widely used surface hopping methods. However, while SCMC was found to be more efficient than other semiclassical methods, it is not yet as efficient as is needed to be used for large molecular systems. Here, we have developed two new methods: the accelerated-SCMC and the accelerated-SCMC with re-Gaussianization, which reduce the cost of the SCMC algorithm up to two orders of magnitude for certain systems. In most cases shown here, the new procedures are nearly as efficient as the commonly used surface hopping schemes, with little to no loss of accuracy. This implies that these modified SCMC algorithms will be of practical numerical solutions for simulating non-adiabatic dynamics in realistic molecular systems.
Non-adiabatic molecular dynamics by accelerated semiclassical Monte Carlo.
White, Alexander J; Gorshkov, Vyacheslav N; Tretiak, Sergei; Mozyrsky, Dmitry
2015-07-01
Non-adiabatic dynamics, where systems non-radiatively transition between electronic states, plays a crucial role in many photo-physical processes, such as fluorescence, phosphorescence, and photoisomerization. Methods for the simulation of non-adiabatic dynamics are typically either numerically impractical, highly complex, or based on approximations which can result in failure for even simple systems. Recently, the Semiclassical Monte Carlo (SCMC) approach was developed in an attempt to combine the accuracy of rigorous semiclassical methods with the efficiency and simplicity of widely used surface hopping methods. However, while SCMC was found to be more efficient than other semiclassical methods, it is not yet as efficient as is needed to be used for large molecular systems. Here, we have developed two new methods: the accelerated-SCMC and the accelerated-SCMC with re-Gaussianization, which reduce the cost of the SCMC algorithm up to two orders of magnitude for certain systems. In most cases shown here, the new procedures are nearly as efficient as the commonly used surface hopping schemes, with little to no loss of accuracy. This implies that these modified SCMC algorithms will be of practical numerical solutions for simulating non-adiabatic dynamics in realistic molecular systems. PMID:26156473
Quantum mechanical molecular dynamics studies of chemical systems
NASA Astrophysics Data System (ADS)
Pavese, Marc
Methods for including quantum mechanical effects in molecular dynamics (MD) simulations are discussed in this thesis. The thesis focuses on the path integral centroid molecular dynamics (CMD) algorithm. This algorithm is first described and then used in simulations of low temperature para-hydrogen, and also in simulations of the excess proton in water clusters and in the bulk. The CMD method allows one to include the effects of nuclear quantization approximately while still maintaining a quasi-classical, trajectory based, description of the dynamics. The effects of quantization of the electronic degrees of freedom are also discussed. These effects are usually taken into account implicitly through parameterized potential functions. However, methods for including the quantum electronic degrees of freedom explicitly in a MD simulation are also discussed in this thesis. Most notably, the Car-Parrinello method, which combines density functional theory (DFT) with MD, is employed with the CMD algorithm. This yields a method which takes explicit account of the quantum electrons and nuclei. Thus, this work represents one feasible approach for considering the quantum nature of all the degrees of freedom of the system while still maintaining an MD framework. In the concluding remarks, future directions and possibilities for this type of approach are discussed.
Non-adiabatic molecular dynamics by accelerated semiclassical Monte Carlo
White, Alexander J.; Gorshkov, Vyacheslav N.; Tretiak, Sergei; Mozyrsky, Dmitry
2015-07-07
Non-adiabatic dynamics, where systems non-radiatively transition between electronic states, plays a crucial role in many photo-physical processes, such as fluorescence, phosphorescence, and photoisomerization. Methods for the simulation of non-adiabatic dynamics are typically either numerically impractical, highly complex, or based on approximations which can result in failure for even simple systems. Recently, the Semiclassical Monte Carlo (SCMC) approach was developed in an attempt to combine the accuracy of rigorous semiclassical methods with the efficiency and simplicity of widely used surface hopping methods. However, while SCMC was found to be more efficient than other semiclassical methods, it is not yet as efficientmore » as is needed to be used for large molecular systems. Here, we have developed two new methods: the accelerated-SCMC and the accelerated-SCMC with re-Gaussianization, which reduce the cost of the SCMC algorithm up to two orders of magnitude for certain systems. In many cases shown here, the new procedures are nearly as efficient as the commonly used surface hopping schemes, with little to no loss of accuracy. This implies that these modified SCMC algorithms will be of practical numerical solutions for simulating non-adiabatic dynamics in realistic molecular systems.« less
Collisional deactivation of CF 3I - a molecular dynamics simulation
NASA Astrophysics Data System (ADS)
Svedung, Harald; Marković, Nikola; Nordholm, Sture
1999-10-01
The detailed mechanisms of ro-vibrational energy transfer in collisions between CF 3I and argon or propane are investigated. Molecular dynamics simulations of collisions between a reactant CF 3I molecule at energies from 50 to 200 kJ/mol with medium argon or propane at selected initial temperatures are interpreted in terms of ergodic collision limits. The intramolecular potential used for CF 3I is a Morse-stretch/harmonic-bend type function with parameters fitted to equilibrium structure, normal mode frequencies and dissociation energies. Simple generic Buckingham type pair-potentials are used for intermolecular atom-atom interactions. Energy transfer is related to (i) geometry of collision, (ii) impact parameter, (iii) number of atom-atom encounters, (iv) average dynamical hardness of interaction at atom-atom collisions, (v) number of minima in the center of mass separation and (vi) lifetime of the collisional complex. The energy transfer in our molecular dynamics calculations is compared with experimental results for the same colliders. The observed trends are interpreted in terms of detailed collisional mechanisms. Our results highlight the importance of rotational excitation and the repulsive part of the intermolecular potential.
Non-adiabatic molecular dynamics by accelerated semiclassical Monte Carlo
White, Alexander J.; Gorshkov, Vyacheslav N.; Tretiak, Sergei; Mozyrsky, Dmitry
2015-07-07
Non-adiabatic dynamics, where systems non-radiatively transition between electronic states, plays a crucial role in many photo-physical processes, such as fluorescence, phosphorescence, and photoisomerization. Methods for the simulation of non-adiabatic dynamics are typically either numerically impractical, highly complex, or based on approximations which can result in failure for even simple systems. Recently, the Semiclassical Monte Carlo (SCMC) approach was developed in an attempt to combine the accuracy of rigorous semiclassical methods with the efficiency and simplicity of widely used surface hopping methods. However, while SCMC was found to be more efficient than other semiclassical methods, it is not yet as efficient as is needed to be used for large molecular systems. Here, we have developed two new methods: the accelerated-SCMC and the accelerated-SCMC with re-Gaussianization, which reduce the cost of the SCMC algorithm up to two orders of magnitude for certain systems. In many cases shown here, the new procedures are nearly as efficient as the commonly used surface hopping schemes, with little to no loss of accuracy. This implies that these modified SCMC algorithms will be of practical numerical solutions for simulating non-adiabatic dynamics in realistic molecular systems.
Modeling and Computer Simulation: Molecular Dynamics and Kinetic Monte Carlo
Wirth, B.D.; Caturla, M.J.; Diaz de la Rubia, T.
2000-10-10
Recent years have witnessed tremendous advances in the realistic multiscale simulation of complex physical phenomena, such as irradiation and aging effects of materials, made possible by the enormous progress achieved in computational physics for calculating reliable, yet tractable interatomic potentials and the vast improvements in computational power and parallel computing. As a result, computational materials science is emerging as an important complement to theory and experiment to provide fundamental materials science insight. This article describes the atomistic modeling techniques of molecular dynamics (MD) and kinetic Monte Carlo (KMC), and an example of their application to radiation damage production and accumulation in metals. It is important to note at the outset that the primary objective of atomistic computer simulation should be obtaining physical insight into atomic-level processes. Classical molecular dynamics is a powerful method for obtaining insight about the dynamics of physical processes that occur on relatively short time scales. Current computational capability allows treatment of atomic systems containing as many as 10{sup 9} atoms for times on the order of 100 ns (10{sup -7}s). The main limitation of classical MD simulation is the relatively short times accessible. Kinetic Monte Carlo provides the ability to reach macroscopic times by modeling diffusional processes and time-scales rather than individual atomic vibrations. Coupling MD and KMC has developed into a powerful, multiscale tool for the simulation of radiation damage in metals.
Kinetic theory molecular dynamics and hot dense matter: theoretical foundations.
Graziani, F R; Bauer, J D; Murillo, M S
2014-09-01
Electrons are weakly coupled in hot, dense matter that is created in high-energy-density experiments. They are also mildly quantum mechanical and the ions associated with them are classical and may be strongly coupled. In addition, the dynamical evolution of plasmas under these hot, dense matter conditions involve a variety of transport and energy exchange processes. Quantum kinetic theory is an ideal tool for treating the electrons but it is not adequate for treating the ions. Molecular dynamics is perfectly suited to describe the classical, strongly coupled ions but not the electrons. We develop a method that combines a Wigner kinetic treatment of the electrons with classical molecular dynamics for the ions. We refer to this hybrid method as "kinetic theory molecular dynamics," or KTMD. The purpose of this paper is to derive KTMD from first principles and place it on a firm theoretical foundation. The framework that KTMD provides for simulating plasmas in the hot, dense regime is particularly useful since current computational methods are generally limited by their inability to treat the dynamical quantum evolution of the electronic component. Using the N-body von Neumann equation for the electron-proton plasma, three variations of KTMD are obtained. Each variant is determined by the physical state of the plasma (e.g., collisional versus collisionless). The first variant of KTMD yields a closed set of equations consisting of a mean-field quantum kinetic equation for the electron one-particle distribution function coupled to a classical Liouville equation for the protons. The latter equation includes both proton-proton Coulombic interactions and an effective electron-proton interaction that involves the convolution of the electron density with the electron-proton Coulomb potential. The mean-field approach is then extended to incorporate equilibrium electron-proton correlations through the Singwi-Tosi-Land-Sjolander (STLS) ansatz. This is the second variant of KTMD
Protons in polar media: An ab initio molecular dynamics study
NASA Astrophysics Data System (ADS)
von Rosenvinge, Tycho
1998-10-01
The hydrates of hydrogen chloride are ionic crystals that contain hydronium (H3O+). The hydronium in the monohydrate has been reported to be statistically disordered between two possible sites related by inversion symmetry. Ab initio molecular dynamics calculations are presented for the monohydrate, as well as the di-, and tri-hydrates, of hydrogen chloride using the density functional based Car-Parrinello technique. The simulations were carried out with the goal of investigating proton disorder in these crystals. The possible role of nuclear quantum effects has been explored via path integral molecular dynamic simulations. The present results suggest that the proposed disordered sites in the monohydrate are dynamically unstable and therefore unlikely to be responsible for the reported disorder. No useful information was obtained for the dihydrate because the large unit cell leads to difficulties in carrying out the simulations. Nuclear quantum effects are shown to be important for characterizing the proton distributions in the trihydrate. The structure and dynamical behavior of liquid HF with dissolved KF have been investigated using the Car- Parrinello ab initio molecular dynamics scheme. Specifically, a system with stoichiometry KFċ2HF was studied at temperatures of 400K and 1000K. This system, which was started from a phase separated mixture, rapidly formed into solvated potassium ions and HnFn+1/sp- polyfluoride anions with n = 1, 2, 3, and 4. The resulting polyfluoride anions were classified, and their structures and dynamical behavior were compared with the known structures and spectra of crystalline compounds KF/cdot xHF and with theoretical predictions of isolated gas phase species. The present study reveals dramatic frequency shifts in the H atom vibrational modes with variation in the HF coordination number of the polyfluoride anion. In particular the FH wagging motion red shifts while the FH stretch blue shifts as n increases. The present calculations
Kinetic theory molecular dynamics and hot dense matter: theoretical foundations.
Graziani, F R; Bauer, J D; Murillo, M S
2014-09-01
Electrons are weakly coupled in hot, dense matter that is created in high-energy-density experiments. They are also mildly quantum mechanical and the ions associated with them are classical and may be strongly coupled. In addition, the dynamical evolution of plasmas under these hot, dense matter conditions involve a variety of transport and energy exchange processes. Quantum kinetic theory is an ideal tool for treating the electrons but it is not adequate for treating the ions. Molecular dynamics is perfectly suited to describe the classical, strongly coupled ions but not the electrons. We develop a method that combines a Wigner kinetic treatment of the electrons with classical molecular dynamics for the ions. We refer to this hybrid method as "kinetic theory molecular dynamics," or KTMD. The purpose of this paper is to derive KTMD from first principles and place it on a firm theoretical foundation. The framework that KTMD provides for simulating plasmas in the hot, dense regime is particularly useful since current computational methods are generally limited by their inability to treat the dynamical quantum evolution of the electronic component. Using the N-body von Neumann equation for the electron-proton plasma, three variations of KTMD are obtained. Each variant is determined by the physical state of the plasma (e.g., collisional versus collisionless). The first variant of KTMD yields a closed set of equations consisting of a mean-field quantum kinetic equation for the electron one-particle distribution function coupled to a classical Liouville equation for the protons. The latter equation includes both proton-proton Coulombic interactions and an effective electron-proton interaction that involves the convolution of the electron density with the electron-proton Coulomb potential. The mean-field approach is then extended to incorporate equilibrium electron-proton correlations through the Singwi-Tosi-Land-Sjolander (STLS) ansatz. This is the second variant of KTMD
Liquid-Phase Exfoliation of Phosphorene: Design Rules from Molecular Dynamics Simulations.
Sresht, Vishnu; Pádua, Agílio A H; Blankschtein, Daniel
2015-08-25
The liquid-phase exfoliation of phosphorene, the two-dimensional derivative of black phosphorus, in the solvents dimethyl sulfoxide (DMSO), dimethylformamide (DMF), isopropyl alcohol, N-methyl-2-pyrrolidone, and N-cyclohexyl-2-pyrrolidone is investigated using three molecular-scale "computer experiments". We modeled solvent-phosphorene interactions using an atomistic force field, based on ab initio calculations and lattice dynamics, that accurately reproduces experimental mechanical properties. We probed solvent molecule ordering at phosphorene/solvent interfaces and discovered that planar molecules such as N-methyl-2-pyrrolidone preferentially orient parallel to the interface. We subsequently measured the energy required to peel a single phosphorene monolayer from a stack of black phosphorus and analyzed the role of "wedges" of solvent molecules intercalating between phosphorene sheets in initiating exfoliation. The exfoliation efficacy of a solvent is enhanced when either molecular planarity "sharpens" this molecular wedge or strong phosphorene-solvent adhesion stabilizes the newly exposed phosphorene surfaces. Finally, we examined the colloidal stability of exfoliated flakes by simulating their aggregation and showed that dispersion is favored when the cohesive energy between the molecules in the solvent monolayer confined between the phosphorene sheets is high (as with DMSO) and is hindered when the adhesion between these molecules and phosphorene is strong; the molecular planarity in solvents like DMF enhances the cohesive energy. Our results are consistent with, and provide a molecular context for, experimental exfoliation studies of phosphorene and other layered solids, and our molecular insights into the significant role of solvent molecular geometry and ordering should complement prevalent solubility-parameter-based approaches in establishing design rules for effective nanomaterial exfoliation media.
Liquid-Phase Exfoliation of Phosphorene: Design Rules from Molecular Dynamics Simulations.
Sresht, Vishnu; Pádua, Agílio A H; Blankschtein, Daniel
2015-08-25
The liquid-phase exfoliation of phosphorene, the two-dimensional derivative of black phosphorus, in the solvents dimethyl sulfoxide (DMSO), dimethylformamide (DMF), isopropyl alcohol, N-methyl-2-pyrrolidone, and N-cyclohexyl-2-pyrrolidone is investigated using three molecular-scale "computer experiments". We modeled solvent-phosphorene interactions using an atomistic force field, based on ab initio calculations and lattice dynamics, that accurately reproduces experimental mechanical properties. We probed solvent molecule ordering at phosphorene/solvent interfaces and discovered that planar molecules such as N-methyl-2-pyrrolidone preferentially orient parallel to the interface. We subsequently measured the energy required to peel a single phosphorene monolayer from a stack of black phosphorus and analyzed the role of "wedges" of solvent molecules intercalating between phosphorene sheets in initiating exfoliation. The exfoliation efficacy of a solvent is enhanced when either molecular planarity "sharpens" this molecular wedge or strong phosphorene-solvent adhesion stabilizes the newly exposed phosphorene surfaces. Finally, we examined the colloidal stability of exfoliated flakes by simulating their aggregation and showed that dispersion is favored when the cohesive energy between the molecules in the solvent monolayer confined between the phosphorene sheets is high (as with DMSO) and is hindered when the adhesion between these molecules and phosphorene is strong; the molecular planarity in solvents like DMF enhances the cohesive energy. Our results are consistent with, and provide a molecular context for, experimental exfoliation studies of phosphorene and other layered solids, and our molecular insights into the significant role of solvent molecular geometry and ordering should complement prevalent solubility-parameter-based approaches in establishing design rules for effective nanomaterial exfoliation media. PMID:26192620
Should thermostatted ring polymer molecular dynamics be used to calculate thermal reaction rates?
Hele, Timothy J. H.; Suleimanov, Yury V.
2015-08-21
We apply Thermostatted Ring Polymer Molecular Dynamics (TRPMD), a recently proposed approximate quantum dynamics method, to the computation of thermal reaction rates. Its short-time transition-state theory limit is identical to rigorous quantum transition-state theory, and we find that its long-time limit is independent of the location of the dividing surface. TRPMD rate theory is then applied to one-dimensional model systems, the atom-diatom bimolecular reactions H + H{sub 2}, D + MuH, and F + H{sub 2}, and the prototypical polyatomic reaction H + CH{sub 4}. Above the crossover temperature, the TRPMD rate is virtually invariant to the strength of the friction applied to the internal ring-polymer normal modes, and beneath the crossover temperature the TRPMD rate generally decreases with increasing friction, in agreement with the predictions of Kramers theory. We therefore find that TRPMD is approximately equal to, or less accurate than, ring polymer molecular dynamics for symmetric reactions, and for certain asymmetric systems and friction parameters closer to the quantum result, providing a basis for further assessment of the accuracy of this method.
Analysis of nucleation using mean first-passage time data from molecular dynamics simulation
NASA Astrophysics Data System (ADS)
Nicholson, David A.; Rutledge, Gregory C.
2016-04-01
We introduce a method for the analysis of nucleation using mean first-passage time (MFPT) statistics obtained by molecular dynamics simulation. The method is based on the Becker-Döring model for the dynamics of a nucleation-mediated phase change and rigorously accounts for the system size dependence of first-passage statistics. It is thus suitable for the analysis of systems in which the separation between time scales for nucleation and growth is small, due to either a small free energy barrier or a large system size. The method is made computationally practical by an approximation of the first-passage time distribution based on its cumulant expansion. Using this approximation, the MFPT of the model can be fit to data from molecular dynamics simulation in order to estimate valuable kinetic parameters, including the free energy barrier, critical nucleus size, and monomer attachment pre-factor, as well as the steady-state rates of nucleation and growth. The method is demonstrated using a case study on nucleation of n-eicosane crystals from the melt. For this system, we found that the observed distribution of first-passage times do not follow an exponential distribution at short times, rendering it incompatible with the assumptions made by some other methods. Using our method, the observed distribution of first-passage times was accurately described, and reasonable estimates for the kinetic parameters and steady-state rates of nucleation and growth were obtained.
NASA Astrophysics Data System (ADS)
Liu, Rumeng; Wang, Lifeng; Jiang, Jingnong
2016-09-01
Thermal vibration of a rectangular single-layered graphene sheet (RSLGS) with initial stress is investigated by a semiquantum molecular dynamics (SQMD) method on the basis of modified Langevin dynamics. The quantum effect in the thermal vibration of RSLGS is accounted by introducing a quantum thermal bath. The spectrum of the thermal vibration of RSLGSs is obtained both by SQMD and classical molecular dynamics (CMD). The RSLGS vibrates with the same frequencies via both the SQMD simulation and the CMD simulation. The root of mean squared (rms) amplitude obtained via the CMD is greater than that obtained via the SQMD. The energy in high order mode is frozen at very low temperature if quantum effect is taken into consideration. An elastic plate model with initial stress considering quantum effects is established to describe the thermal vibration of the RSLGS. The rms amplitude of RSLGS calculated by plate model with the law of energy equipartition and that obtained from the CMD coincide very well. The plate model considering the quantum effects provides accurate prediction of the rms amplitude of the RSLGS obtained from the SQMD. These results indicate that quantum effects cannot be neglected in the thermal vibration of the RSLGS at low temperature case.
Molecular stopwatches, cogwheels and ``spinflakes'': studying the dynamics of molecular superrotors
NASA Astrophysics Data System (ADS)
Korobenko, Aleksey; Milner, Alexander; Hepburn, John; Milner, Valery
2015-05-01
Using the technique of an optical centrifuge, we excite diatomic molecules to ultrafast synchronous rotation. Femtosecond velocity-map imaging allows us to visualize and study the coherent dynamics of molecular superrotors under field free conditions and in external magnetic field. We demonstrate that when the created rotational wave packet is narrow, its free evolution is nondispersing and follows the motion of a classically rotating dumbbell or a hand of the smallest natural stopwatch. For wider rotational distributions, we observe the breakdown of classical rotation, when a dumbbell shape changes to that of a ``quantum cogwheel'' - a molecular state simultaneously aligned along multiple direction. Our measurements in external magnetic field reveal other peculiar aspects of the rich dynamics of molecular superrotors. The rotation of a non-magnetic molecule interacts with the applied field only weakly, giving rise to slow precession of the molecular angular momentum around the field direction. In contrast, the electronic spin of a paramagnetic superrotor mediates this interaction, causing the initial disk-like angular distribution to split into several spatial components, each precessing with its own frequency determined by the spin projection.
Omelyan, Igor P; Kovalenko, Andriy
2012-01-10
We propose and validate a new multiscale technique, the extrapolative isokinetic Nóse-Hoover chain orientational (EINO) motion multiple time step algorithm for rigid interaction site models of molecular liquids. It nontrivially combines the multiple time step decomposition operator method with a specific extrapolation of intermolecular interactions, complemented by an extended isokinetic Nosé-Hoover chain approach in the presence of translational and orientational degrees of freedom. The EINO algorithm obviates the limitations on time step size in molecular dynamics simulations. While the best existing multistep algorithms can advance from a 5 fs single step to a maximum 100 fs outer step, we show on the basis of molecular dynamics simulations of the TIP4P water that our EINO technique overcomes this barrier. Specifically, we have achieved giant time steps on the order of 500 fs up to 5 ps, which now become available in the study of equilibrium and conformational properties of molecular liquids without a loss of stability and accuracy.
Dynamics of Nanoscale Grain-Boundary Decohesion in Aluminum by Molecular-Dynamics Simulation
NASA Technical Reports Server (NTRS)
Yamakov, V.; Saether, E.; Phillips, D. R.; Glaessegen, E. H.
2007-01-01
The dynamics and energetics of intergranular crack growth along a flat grain boundary in aluminum is studied by a molecular-dynamics simulation model for crack propagation under steady-state conditions. Using the ability of the molecular-dynamics simulation to identify atoms involved in different atomistic mechanisms, it was possible to identify the energy contribution of different processes taking place during crack growth. The energy contributions were divided as: elastic energy, defined as the potential energy of the atoms in fcc crystallographic state; and plastically stored energy, the energy of stacking faults and twin boundaries; grain-boundary and surface energy. In addition, monitoring the amount of heat exchange with the molecular-dynamics thermostat gives the energy dissipated as heat in the system. The energetic analysis indicates that the majority of energy in a fast growing crack is dissipated as heat. This dissipation increases linearly at low speed, and faster than linear at speeds approaching 1/3 the Rayleigh wave speed when the crack tip becomes dynamically unstable producing periodic dislocation bursts until the crack is blunted.
Fang, Wanping; Meinhardt, Lyndel W; Mischke, Sue; Bellato, Cláudia M; Motilal, Lambert; Zhang, Dapeng
2014-01-15
Cacao (Theobroma cacao L.), the source of cocoa, is an economically important tropical crop. One problem with the premium cacao market is contamination with off-types adulterating raw premium material. Accurate determination of the genetic identity of single cacao beans is essential for ensuring cocoa authentication. Using nanofluidic single nucleotide polymorphism (SNP) genotyping with 48 SNP markers, we generated SNP fingerprints for small quantities of DNA extracted from the seed coat of single cacao beans. On the basis of the SNP profiles, we identified an assumed adulterant variety, which was unambiguously distinguished from the authentic beans by multilocus matching. Assignment tests based on both Bayesian clustering analysis and allele frequency clearly separated all 30 authentic samples from the non-authentic samples. Distance-based principle coordinate analysis further supported these results. The nanofluidic SNP protocol, together with forensic statistical tools, is sufficiently robust to establish authentication and to verify gourmet cacao varieties. This method shows significant potential for practical application.
The route to MBxNyCz molecular wheels: II. Results using accurate functionals and basis sets
NASA Astrophysics Data System (ADS)
Güthler, A.; Mukhopadhyay, S.; Pandey, R.; Boustani, I.
2014-04-01
Applying ab initio quantum chemical methods, molecular wheels composed of metal and light atoms were investigated. High quality basis sets 6-31G*, TZPV, and cc-pVTZ as well as exchange and non-local correlation functionals B3LYP, BP86 and B3P86 were used. The ground-state energy and structures of cyclic planar and pyramidal clusters TiBn (for n = 3-10) were computed. In addition, the relative stability and electronic structures of molecular wheels TiBxNyCz (for x, y, z = 0-10) and MBnC10-n (for n = 2 to 5 and M = Sc to Zn) were determined. This paper sustains a follow-up study to the previous one of Boustani and Pandey [Solid State Sci. 14 (2012) 1591], in which the calculations were carried out at the HF-SCF/STO3G/6-31G level of theory to determine the initial stability and properties. The results show that there is a competition between the 2D planar and the 3D pyramidal TiBn clusters (for n = 3-8). Different isomers of TiB10 clusters were also studied and a structural transition of 3D-isomer into 2D-wheel is presented. Substitution boron in TiB10 by carbon or/and nitrogen atoms enhances the stability and leads toward the most stable wheel TiB3C7. Furthermore, the computations show that Sc, Ti and V at the center of the molecular wheels are energetically favored over other transition metal atoms of the first row.
Molecular Dynamics Simulations of Fracture of Model Epoxies
STEVENS,MARK J.
2000-01-18
The failure of thermosetting polymer adhesives is an important problem which particularly lacks understanding from the molecular viewpoint. While linear elastic fracture mechanics works well for such polymers far from the crack tip, the method breaks down near the crack tip where large plastic deformation occurs and the molecular details become important [1]. Results of molecular dynamics simulations of highly crosslinked polymer networks bonded to a solid surface are presented here. Epoxies are used as the guide for modeling. The focus of the simulations is the network connectivity and the interfacial strength. In a random network, the bond stress is expected to vary, and the most stressed bonds will break first [2]. Crack initiation should occur where a cluster of highly constrained bonds exists. There is no reason to expect crack initiation to occur at the interface. The results to be presented show that the solid surface limits the interfacial bonding resulting in stressed interfacial bonds and interfacial fracture. The bonds in highly-crosslinked random networks do not become stressed as expected. The sequence of molecular structural deformations that lead to failure has been determined and found to be strongly dependent upon the network connectivity. The structure of these networks and its influence on the stress-strain behavior will be discussed in general. A set of ideal, ordered networks have been constructed to manipulate the deformation sequence to achieve different fracture modes (i.e. cohesive vs. adhesive).
Nanochannel flow past permeable walls via molecular dynamics
NASA Astrophysics Data System (ADS)
Xie, Jian-Fei; Cao, Bing-Yang
2016-07-01
The nanochannel flow past permeable walls with nanopores is investigated by molecular dynamics (MD) simulations, including the density distribution, velocity field, molecular penetration mechanism and surface friction coefficient. A low density distribution has been found at the gas-wall interface demonstrating the low pressure region. In addition, there exists a jump of the gas density on the permeable surface, which indicates the discontinuity of the density distribution across the permeable surface. On the other hand, the nanoscale vortices are observed in nanopores of the permeable wall, and the reduced mass flux of the flow in nanopores results in a shifted hydrodynamic boundary above the permeable surface. Particularly the slip length of the gas flow on the permeable surface is pronounced a non-linear function of the molecular mean free path, which produces a large value of the tangential momentum accommodation coefficient (TMAC) and a big portion of the diffusive refection. Moreover, the gas-gas interaction and multi-collision among gas molecules may take place in nanopores, which contribute to large values of TMAC. Consequently the boundary friction coefficient on the permeable surface is increased because of the energy dissipation consumed by the nanoscale vortices in nanopores. The molecular boundary condition provides us with a new picture of the nanochannel flow past the permeable wall with nanopores.
Implementation of Green's function molecular dynamics: An extension to LAMMPS
NASA Astrophysics Data System (ADS)
Kong, Ling Ti; Bartels, Guido; Campañá, Carlos; Denniston, Colin; Müser, Martin H.
2009-06-01
The Green's function molecular dynamics method, which enables one to study the elastic response of a three-dimensional solid to an external stress field by taking into consideration only the surface atoms, was implemented as an extension to an open source classical molecular dynamics simulation code LAMMPS. This was done in the style of fixes. The first fix, FixGFC, measures the elastic stiffness coefficients for a (small) solid block of a given material by making use of the fluctuation-dissipation theorem. With the help of the second fix, FixGFMD, the coefficients obtained from FixGFC can then be used to compute the elastic forces for a (large) block of the same material. Both fixes are designed to be run in parallel and to exploit the functions provided by LAMMPS. Program summaryProgram title: FixGFC/FixGFMD Catalogue identifier: AECW_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AECW_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: yes No. of lines in distributed program, including test data, etc.: 33 469 No. of bytes in distributed program, including test data, etc.: 1 383 631 Distribution format: tar.gz Programming language: C++ Computer: All Operating system: Linux Has the code been vectorized or parallelized?: Parallelized via MPI RAM: Depends on the problem Classification: 7.7 External routines: MPI, FFTW 2.1.5 ( http://www.fftw.org/), LAMMPS version May 21, 2008 ( http://lammps.sandia.gov/) Nature of problem: Using molecular dynamics to study elastically deforming solids imposes very high computational costs because portions of the solid far away from the interface or contact points need to be included in the simulation to reproduce the effects of long-range elastic deformations. Green's function molecular dynamics (GFMD) incorporates the full elastic response of semi-infinite solids so that only surface atoms have to be considered in molecular dynamics simulations, thus
Quantum molecular dynamics simulations of thermophysical properties of fluid ethane
NASA Astrophysics Data System (ADS)
Zhang, Yujuan; Wang, Cong; Zheng, Fawei; Zhang, Ping
2012-12-01
We have performed first-principles molecular-dynamics simulations based on density-functional theory to study the thermophysical properties of ethane under extreme conditions. We present results for the equation of state of fluid ethane in the warm dense region. The optical conductivity is calculated via the Kubo-Greenwood formula from which the dc conductivity and optical reflectivity are derived. The close correlation between the nonmetal-metal transition of ethane and its decomposition, that ethane dissociates significantly into molecular and/or atomic hydrogen and some long alkane chains, has been systematically studied by analyzing the optical conductivity spectra, pair correlation functions, electronic density of states, and charge density distribution of fluid ethane.
Thermal Transport in Carbon Nanotubes using Molecular Dynamics
NASA Astrophysics Data System (ADS)
Moore, Andrew; Khatun, Mahfuza
2011-10-01
We will present results of thermal transport phenomena in Carbon Nanotube (CNT) structures. CNTs have many interesting physical properties, and have the potential for device applications. Specifically, CNTs are robust materials with high thermal conductance and excellent electrical conduction properties. A review of electrical and thermal conduction of the structures will be discussed. The research requires analytical analysis as well as simulation. The major thrust of this study is the usage of the molecular dynamics (MD) simulator, LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator). A significant investigation using the LAMMPS code is conducted on the existing Beowulf Computing Cluster at BSU. NanoHUB, an open online resource to the entire nanotechnology community developed by the researchers of Purdue University, is used for further supplementary resources. Results will include the time-dependence of temperature, kinetic energy, potential energy, heat flux correlation, and heat conduction.
Permeance of H2 through porous graphene from molecular dynamics
NASA Astrophysics Data System (ADS)
Liu, Hongjun; Dai, Sheng; Jiang, De-en
2013-12-01
A recent experiment (Koenig et al., 2012 [15]) demonstrated the capability of porous graphene as one-atom-thin membrane to separate gases by molecular sieving. A quantitative connection between the measured leak rate and the simulated gas permeance has yet to be established. Using H2 as a model gas, here we determine its permeance through porous graphene from molecular dynamics (MD) simulations. Trajectories are used to directly obtain H2 flux, pressure drop across the graphene membrane, and subsequently, H2 permeance. The permeance is determined to be on the order of 105 GPU (gas permeance unit) for pressure driving forces ranging from 2 to 163 atm. By relating to the experimental leak rate, we then use the permeation data to estimate the pore density in the experimentally created porous graphene.