WorldWideScience

Sample records for water molecular dynamics

  1. Molecular dynamics simulation of a polysorbate 80 micelle in water

    NARCIS (Netherlands)

    Amani, Amir; York, Peter; de Waard, Hans; Anwar, Jamshed

    2011-01-01

    The structure and dynamics of a single molecule of the nonionic surfactant polysorbate 80 (POE (20) sorbitan monooleate; Tween 80 (R)) as well as a micelle comprising sixty molecules of polysorbate 80 in water have been investigated by molecular dynamics simulation. In its free state in water the po

  2. Molecular dynamics insights into human aquaporin 2 water channel.

    Science.gov (United States)

    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.

  3. Adsorbed water on iron surface by molecular dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Fernandes, F.W.; Campos, T.M.B.; Cividanes, L.S., E-mail: flaviano@ita.br; Simonetti, E.A.N.; Thim, G.P.

    2016-01-30

    Graphical abstract: - Highlights: • We developed a new force field to describe the Fe–H{sub 2}O interaction. • We developed a new force field to describe the flexible water model at low temperature. • We analyze the orientation of water along the iron surface. • We calculate the vibrational spectra of water near the iron surface. • We found a complex relationship between water orientation and the atomic vibrational spectra at different sites of adsorption along the iron surface. - Abstract: The adsorption of H{sub 2}O molecules on metal surfaces is important to understand the early process of water corrosion. This process can be described by computational simulation using molecular dynamics and Monte Carlo. However, this simulation demands an efficient description of the surface interactions between the water molecule and the metallic surface. In this study, an effective force field to describe the iron-water surface interactions was developed and it was used in a molecular dynamics simulation. The results showed a very good agreement between the simulated vibrational-DOS spectrum and the experimental vibrational spectrum of the iron–water interface. The water density profile revealed the presence of a water double layer in the metal interface. Furthermore, the horizontal mapping combined with the angular distribution of the molecular plane allowed the analysis of the water structure above the surface, which in turn agrees with the model of the double layer on metal surfaces.

  4. Molecular Dynamics Simulations of Water Nanodroplets on Silica Surfaces

    DEFF Research Database (Denmark)

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

    2009-01-01

    and DNA microarrays technologies.4,5,6,7,8 Although extensive experimental, theoretical and computational work has been devoted to study the nature of the interaction between silica and water,2,9-16 at the molecular level a complete understanding of silica-water systems has not been reached. Contact angle...... computations of water droplets on silica surfaces offers a useful fundamental and quantitative measurement in order to study chemical and physical properties of water-silica systems.3,16,17,18 For hydrophobic systems the static and dynamic properties of the fluid-solid interface are influenced by the presence...

  5. Molecular dynamics study of the water/n-alkane interface

    Institute of Scientific and Technical Information of China (English)

    2010-01-01

    Molecular dynamics simulations on the interface between liquid water and liquid n-alkane (including octane, nonane, decane, undecane and dodecane) have been performed with the purpose to study the interfacial properties: (Ⅰ) density profile; (Ⅱ) molecular orientation; (Ⅲ) interfacial tension and the temperature effect on the interfacial tension. Simulation results show that at the interface the structures of both water and n-alkane are different from those in the bulk. Water has an orientational preference due to the number of hydrogen bonds per molecule maximized. N-alkane has a more lateral orientation with respect to the interface in order to be in close contact with water. The calculated individual phase bulk density and interfacial tension of water/n-alkane systems are in good agreement with the corresponding experimental ones.

  6. Molecular dynamic simulations of the water absorbency of hydrogels.

    Science.gov (United States)

    Ou, Xiang; Han, Qiang; Dai, Hui-Hui; Wang, Jiong

    2015-09-01

    A polymer gel can imbibe solvent molecules through surface tension effect. When the solvent happens to be water, the gel can swell to a large extent and forms an aggregate called hydrogel. The large deformation caused by such swelling makes it difficult to study the behaviors of hydrogels. Currently, few molecular dynamic simulation works have been reported on the water absorbing mechanism of hydrogels. In this paper, we first use molecular dynamic simulation to study the water absorbing mechanism of hydrogels and propose a hydrogel-water interface model to study the water absorbency of the hydrogel surface. Also, the saturated water content and volume expansion rate of the hydrogel are investigated by building a hydrogel model with different cross-linking degree and by comparing the water absorption curves under different temperatures. The sample hydrogel model used consists of Polyethylene glycol diglycidyl ether (PEGDGE) as epoxy and the Jeffamine, poly-oxy-alkylene-amines, as curing agent. The conclusions obtained are useful for further investigation on PEGDGE/Jeffamine hydrogel. Moreover, the simulation methods, including hydrogel-water interface modeling, we first propose are also suitable to study the water absorbing mechanism of other hydrogels.

  7. Molecular Dynamics Simulation of Water Confined in Carbon Nanotubes

    Institute of Scientific and Technical Information of China (English)

    WANG Yan; YUAN Hong-Jun

    2007-01-01

    Molecular dynamics simulations are performed for water conGned in carbon nanotubes with various diameters (11.0-13.8 A). The simulations under an isobaric pressure (one atmosphere) by lowering temperatures from 300K to 190 K are carried out. Water molecules within variously sized tubes tend to transform from disorder to order with different configurations (four-water-molecule ring, six-water-molecule ring and seven-water-molecule ring) at phase transition temperatures, which may be lowered by the increasing tube radius. It is also found that the configurations of water in (10, 10) tube are not unique (seven-molecule ring and seven-molecule ring plus water chain).

  8. Variational path integral molecular dynamics study of a water molecule

    Science.gov (United States)

    Miura, Shinichi

    2013-08-01

    In the present study, a variational path integral molecular dynamics method developed by the author [Chem. Phys. Lett. 482, 165 (2009)] is applied to a water molecule on the adiabatic potential energy surface. The method numerically generates an exact wavefunction using a trial wavefunction of the target system. It has been shown that even if a poor trial wavefunction is employed, the exact quantum distribution is numerically extracted, demonstrating the robustness of the variational path integral method.

  9. Molecular dynamics simulations of water within models of ion channels.

    Science.gov (United States)

    Breed, J; Sankararamakrishnan, R; Kerr, I D; Sansom, M S

    1996-04-01

    The transbilayer pores formed by ion channel proteins contain extended columns of water molecules. The dynamic properties of such waters have been suggested to differ from those of water in its bulk state. Molecular dynamics simulations of ion channel models solvated within and at the mouths of their pores are used to investigate the dynamics and structure of intra-pore water. Three classes of channel model are investigated: a) parallel bundles of hydrophobic (Ala20) alpha-helices; b) eight-stranded hydrophobic (Ala10) antiparallel beta-barrels; and c) parallel bundles of amphipathic alpha-helices (namely, delta-toxin, alamethicin, and nicotinic acetylcholine receptor M2 helix). The self-diffusion coefficients of water molecules within the pores are reduced significantly relative to bulk water in all of the models. Water rotational reorientation rates are also reduced within the pores, particularly in those pores formed by alpha-helix bundles. In the narrowest pore (that of the Ala20 pentameric helix bundle) self-diffusion coefficients and reorientation rates of intra-pore waters are reduced by approximately an order of magnitude relative to bulk solvent. In Ala20 helix bundles the water dipoles orient antiparallel to the helix dipoles. Such dipole/dipole interaction between water and pore may explain how water-filled ion channels may be formed by hydrophobic helices. In the bundles of amphipathic helices the orientation of water dipoles is modulated by the presence of charged side chains. No preferential orientation of water dipoles relative to the pore axis is observed in the hydrophobic beta-barrel models.

  10. Understanding water: Molecular dynamics simulations of solubilized and crystallized myoglobin

    Energy Technology Data Exchange (ETDEWEB)

    Wei Gu; Garcia, A.E.; Schoenborn, B.P. [Los Alamos National Laboratory, NM (United States)

    1994-12-31

    Molecular dynamics simulations were performed on CO myoglobin to evaluate the stability of the bound water molecules as determined in a neutron diffraction analysis. The myoglobin structure derived from the neutron analysis provided the starting coordinate set used in the simulations. The simulations show that only a few water molecules are tightly bound to protein atoms, while most solvent molecules are labile, breaking and reforming hydrogen bonds. Comparison between myoglobin in solution and in a single crystal highlighted some of the packing effects on the solvent structure and shows that water solvent plays an indispensable role in protein dynamics and structural stability. The described observations explain some of the differences in the experimental results of protein hydration as observed in NMR, neutron and X-ray diffraction studies.

  11. Molecular Dynamics Investigation of Benzene in Supercritical Water

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    Microscopic structure and diffusion properties of benzene in ambient water (298 K, 0.1 MPa) and super critical water (673-773 K, 25-35 MPa) are investigated by molecular dynamics simulation with site-site models. It is found that at the ambient condition, the water molecules surrounding a benzene molecule form a hydrogen bond network. The hydrogen bond interaction between supercritical water molecules decreases dramatically under supercritical conditions. The diffusion coefficients of both the solute molecule and solvent molecule at supercritical conditions increase by 30-180 times than those at the ambient condition. With the temperature approaching the critical temperature, the change of diffusion coefficient with pressure becomes pronounced.

  12. Molecular Dynamics Simulations of Carbon Nanotubes in Water

    Science.gov (United States)

    Walther, J. H.; Jaffe, R.; Halicioglu, T.; Koumoutsakos, P.

    2000-01-01

    We study the hydrophobic/hydrophilic behavior of carbon nanotubes using molecular dynamics simulations. The energetics of the carbon-water interface are mainly dispersive but in the present study augmented with a carbon quadrupole term acting on the charge sites of the water. The simulations indicate that this contribution is negligible in terms of modifying the structural properties of water at the interface. Simulations of two carbon nanotubes in water display a wetting and drying of the interface between the nanotubes depending on their initial spacing. Thus, initial tube spacings of 7 and 8 A resulted in a drying of the interface whereas spacing of > 9 A remain wet during the course of the simulation. Finally, we present a novel particle-particle-particle-mesh algorithm for long range potentials which allows for general (curvilinear) meshes and "black-box" fast solvers by adopting an influence matrix technique.

  13. Molecular Dynamics Simulations of Carbon Nanotubes in Water

    Science.gov (United States)

    Walther, J. H.; Jaffe, R.; Halicioglu, T.; Koumoutsakos, P.

    2000-01-01

    We study the hydrophobic/hydrophilic behavior of carbon nanotubes using molecular dynamics simulations. The energetics of the carbon-water interface are mainly dispersive but in the present study augmented with a carbon quadrupole term acting on the charge sites of the water. The simulations indicate that this contribution is negligible in terms of modifying the structural properties of water at the interface. Simulations of two carbon nanotubes in water display a wetting and drying of the interface between the nanotubes depending on their initial spacing. Thus, initial tube spacings of 7 and 8 A resulted in a drying of the interface whereas spacing of > 9 A remain wet during the course of the simulation. Finally, we present a novel particle-particle-particle-mesh algorithm for long range potentials which allows for general (curvilinear) meshes and "black-box" fast solvers by adopting an influence matrix technique.

  14. Molecular dynamics of water at high temperatures and pressures

    Science.gov (United States)

    Brodholt, John; Wood, Bernard

    1990-09-01

    There are currently no precise P-V-T data for water at pressures above 8.9 kbars and temperatures above 900°C. Many petrological processes in the lower crust and upper mantle take place under more extreme conditions, however and petrologists commonly rely on empirical equations of state such as the modified Redlich-Kwong equation (MRK) to extrapolate the low pressure data. In this study we have taken an alternative approach and attempted to simulate the P-V-T properties of water using molecular dynamics. The TIP4P intermolecular potential for H 2O ( JORGENSEN et al., 1983) has had considerable success predicting the properties of water at low temperatures and pressures up to 10 kbar ( MADURA et al., 1988). We have extended its application by making molecular dynamics (MD) simulations at a density of 1.0 g/cc from 300 to 2300 K and 0.5 to 40 kbars. The results agree with the P-V-T data of BURNHAM et al. (1969) (up to 10 kbars) with an average error of under 2%. This is a much better concordance than is obtained with any of the currently used versions of MRK. At 300 kbars and 2000 K the MD simulations predict densities within 8% of those obtained in the shock wave experiments of KORMER (1968). This is a very good agreement given the fact that water ionizes to some extent at high pressures ( MITCHELL and NELLIS, 1982) and we have made no provisions for this effect. We conclude that molecular dynamics simulations provide the possibility of estimating P-V-T properties in the upper mantle P-T regime with very good accuracy.

  15. Molecular dynamics of the water liquid-vapor interface

    Science.gov (United States)

    Wilson, M. A.; Pohorille, A.; Pratt, L. R.; MacElroy, R. D. (Principal Investigator)

    1987-01-01

    The results of molecular dynamics calculations on the equilibrium interface between liquid water and its vapor at 325 K are presented. For the TIP4P model of water intermolecular pair potentials, the average surface dipole density points from the vapor to the liquid. The most common orientations of water molecules have the C2 nu molecular axis roughly parallel to the interface. The distributions are quite broad and therefore compatible with the intermolecular correlations characteristic of bulk liquid water. All near-neighbor pairs in the outermost interfacial layers are hydrogen bonded according to the common definition adopted here. The orientational preferences of water molecules near a free surface differ from those near rigidly planar walls which can be interpreted in terms of patterns found in hexagonal ice 1. The mean electric field in the interfacial region is parallel to the mean polarization which indicates that attention cannot be limited to dipolar charge distributions in macroscopic descriptions of the electrical properties of this interface. The value of the surface tension obtained is 132 +/- 46 dyn/cm, significantly different from the value for experimental water of 68 dyn/cm at 325 K.

  16. Molecular dynamics of the water liquid-vapor interface

    Science.gov (United States)

    Wilson, M. A.; Pohorille, A.; Pratt, L. R.; MacElroy, R. D. (Principal Investigator)

    1987-01-01

    The results of molecular dynamics calculations on the equilibrium interface between liquid water and its vapor at 325 K are presented. For the TIP4P model of water intermolecular pair potentials, the average surface dipole density points from the vapor to the liquid. The most common orientations of water molecules have the C2 nu molecular axis roughly parallel to the interface. The distributions are quite broad and therefore compatible with the intermolecular correlations characteristic of bulk liquid water. All near-neighbor pairs in the outermost interfacial layers are hydrogen bonded according to the common definition adopted here. The orientational preferences of water molecules near a free surface differ from those near rigidly planar walls which can be interpreted in terms of patterns found in hexagonal ice 1. The mean electric field in the interfacial region is parallel to the mean polarization which indicates that attention cannot be limited to dipolar charge distributions in macroscopic descriptions of the electrical properties of this interface. The value of the surface tension obtained is 132 +/- 46 dyn/cm, significantly different from the value for experimental water of 68 dyn/cm at 325 K.

  17. A molecular dynamics study on surface properties of supercooled water

    Institute of Scientific and Technical Information of China (English)

    L(U) Yongjun; WEI Bingbo

    2006-01-01

    Molecular dynamics simulations were performed to study the surface properties of water in a temperature range from 228 to 293 K by using the extended simple point charge (SPC/E) and four-site TIP4P potentials. The calculated surface tension increases with the decrease of temperature, and moreover the slopes of the surface tension-temperature curves show a weak rise below 273 K, whereas no obvious anomalies appear near 228 K, which accords with the previous experiments. Compared with the measured values, the SPC/E potential shows a good agreement, and the TIP4P potential scription of the surface structure of supercooled water for the SPC/E. When simulating the orientational distributions of water molecules near the surface, the SPC/E potential produces higher ordering and larger surface potentials than the TIP4P potential.

  18. Simulation of carbohydrates, from molecular docking to dynamics in water.

    Science.gov (United States)

    Sapay, Nicolas; Nurisso, Alessandra; Imberty, Anne

    2013-01-01

    Modeling of carbohydrates is particularly challenging because of the variety of structures resulting for the high number of monosaccharides and possible linkages and also because of their intrinsic flexibility. The development of carbohydrate parameters for molecular modeling is still an active field. Nowadays, main carbohydrates force fields are GLYCAM06, CHARMM36, and GROMOS 45A4. GLYCAM06 includes the largest choice of compounds and is compatible with the AMBER force fields and associated. Furthermore, AMBER includes tools for the implementation of new parameters. When looking at protein-carbohydrate interaction, the choice of the starting structure is of importance. Such complex can be sometimes obtained from the Protein Data Bank-although the stereochemistry of sugars may require some corrections. When no experimental data is available, molecular docking simulation is generally used to the obtain protein-carbohydrate complex coordinates. As molecular docking parameters are not specifically dedicated to carbohydrates, inaccuracies should be expected, especially for the docking of polysaccharides. This issue can be addressed at least partially by combining molecular docking with molecular dynamics simulation in water.

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

    DEFF Research Database (Denmark)

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

    2012-01-01

    In nonaqueous enzymology, control of enzyme hydration is commonly approached by fixing the thermodynamic water activity of the medium. In this work, we present a strategy for evaluating the water activity in molecular dynamics simulations of proteins in water/organic solvent mixtures. The method...... relies on determining the water content of the bulk phase and uses a combination of Kirkwood−Buff theory and free energy calculations to determine corresponding activity coefficients. We apply the method in a molecular dynamics study of Candida antarctica lipase B in pure water and the organic solvents...... methanol, tert-butyl alcohol, methyl tert-butyl ether, and hexane, each mixture at five different water activities. It is shown that similar water activity yields similar enzyme hydration in the different solvents. However, both solvent and water activity are shown to have profound effects on enzyme...

  20. A molecular dynamics study on surface properties of supercooled water

    Institute of Scientific and Technical Information of China (English)

    Lü; Yongjun

    2006-01-01

    [1]Basu J K,Hazra S,Sanyal M K.Growth mechanism of Langmuir-Blodgett films.Phys Rev Lett,1999,82:4675-4678[2]Taylor R S,Shields R L.Molecular-dynamics simulations of the ethanol liquid-vapor interface.J Chem Phys,2003,119:12569-12576[3]Velev O D,Gurkov T D,Ivanov I B,et al.Abnormal thickness and stability of nonequilibrium liquid films.Phys Rev Lett,1995,75:264-267[4]Weng J G,Park S,Lukes J R,et al.Molecular dynamics investigation of thickness effect on liquid films.J Chem Phys,2000,113:5917-5923[5]Zakharov V V,Brodskaya E N,Laaksonen A.Surface tension of water droplets:A molecular dynamics study of model and size dependencies.J Chem Phys,1997,107:10675-10683[6]Wang J Z,Chen M,Guo Z Y.A two-dimensional molecular dynamics simulation of liquid-vapor nucleation.Chin Sci Bull,2003,48(7):623-626[7]Guissani Y,Guillot B.A computer simulation study of the liquid-vapor coexistence curve of water.J Chem Phys,1993,98:8221-8235[8]Wilson M A,Pohorille A,Pratt L R.Surface potential of the water liquid-vapor interface.J Chem Phys,1988,88:3281-3285[9]Alejandre J,Tildesley D J,Chapela G A.Molecular dynamics simulation of the orthobaric densities and surface tension of water.J Chem Phys,1995,102:4574-4583[10]Matsumoto M,Kataoka Y.Study on liquid-vapor interface of water (Ⅰ):Simulational results of thermodynamic properties and orientational structure.J Chem Phys,1988,88:3233-3245[11]Floriano M A,Angell C A.Surface tension and molar surface free energy and entropy of water to-27.2℃.J Phys Chem,1990,94:4199-4202[12]Jorgensen W L,Chandrasekhar J,Madura J D.Comparison of simple potential functions for simulating liquid water.J Chem Phys,1993,79:926-935[13]Berendsen H J C,Grigera J R,Straatsma T P.The missing term in effective pair potentials.J Phys Chem,1987,91:6269-6271[14]Arbuckle B W,Clancy P.Effects of the Ewald sum on the free energy of the extended simple point charge model for water.J Chem Phys,2002,116:5090-5098[15]Tarazona P,Chacon E,Reinaldo-Falagan M,et al

  1. Molecular dynamics simulations of radon accumulation in water and oil

    Energy Technology Data Exchange (ETDEWEB)

    Pafong, Elvira; Drossel, Barbara [Institut fuer Festkoerperphysik, Technische Universitaet Darmstadt (Germany)

    2016-07-01

    Radon is a radioactive gas that can enter the human body from air or from ground water. Radon can accumulate to levels that considerably rise the risk of lung cancer while it is also known as a a treatment of various ailments, most notably rheumatoid arthritis. The accumulation of radon differs between tissues, with particularly high concentrations in fatty cells. In order to understand the mechanisms responsible for the different solubility of radon in water and fat, we perform molecular dynamics simulations of radon gas at ambient conditions in contact with a bulk material consisting either of water or oil. We evaluate the diffusion coefficient of radon in both media as well as the equilibrium concentration. The crucial point here is to understand the hydrophobic interaction between water and radon as compared to the dispersive interaction between radon and oil. Therefore, we artificially vary the water charges (i.e., the hydrophobicity) as well as the parameters of the van-der-Waals interaction.

  2. Water dynamics in protein hydration shells: the molecular origins of the dynamical perturbation.

    Science.gov (United States)

    Fogarty, Aoife C; Laage, Damien

    2014-07-17

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

  3. Photodesorption of water ice: a molecular dynamics study

    CERN Document Server

    Andersson, S

    2008-01-01

    Absorption of ultraviolet radiation by water ice coating interstellar grains can lead to dissociation and desorption of the ice molecules. These processes are thought to be important in the gas-grain chemistry in molecular clouds and protoplanetary disks, but very few quantitative studies exist. We compute the photodesorption efficiencies of amorphous water ice and elucidate the mechanisms by which desorption occurs. Classical molecular dynamics calculations were performed for a compact amorphous ice surface at 10 K thought to be representative of interstellar ice. Dissociation and desorption of H2O molecules in the top six monolayers are considered following absorption into the first excited electronic state with photons in the 1300-1500 Angstrom range. The trajectories of the H and OH photofragments are followed until they escape or become trapped in the ice. The probability for H2O desorption per absorbed UV photon is 0.5-1% in the top three monolayers, then decreases to 0.03% in the next two monolayers, a...

  4. Molecular Dynamics of a Water-Lipid Bilayer Interface

    Science.gov (United States)

    Wilson, Michael A.; Pohorille, Andrew

    1994-01-01

    We present results of molecular dynamics simulations of a glycerol 1-monooleate bilayer in water. The total length of analyzed trajectories is 5ns. The calculated width of the bilayer agrees well with the experimentally measured value. The interior of the membrane is in a highly disordered fluid state. Atomic density profile, orientational and conformational distribution functions, and order parameters indicate that disorder increases toward the center of the bilayer. Analysis of out-of-plane thermal fluctuations of the bilayer surfaces occurring at the time scale of the present calculations reveals that the distribution of modes agrees with predictions of the capillary wave model. Fluctuations of both bilayer surfaces are uncorrelated, yielding Gaussian distribution of instantaneous widths of the membrane. Fluctuations of the width produce transient thinning defects in the bilayer which occasionally span almost half of the membrane. The leading mechanism of these fluctuations is the orientational and conformational motion of head groups rather than vertical motion of the whole molecules. Water considerably penetrates the head group region of the bilayer but not its hydrocarbon core. The total net excess dipole moment of the interfacial water points toward the aqueous phase, but the water polarization profile is non-monotonic. Both water and head groups significantly contribute to the surface potential across the interface. The calculated sign of the surface potential is in agreement with that from experimental measurements, but the value is markedly overestimated. The structural and electrical properties of the water-bilayer system are discussed in relation to membrane functions, in particular transport of ions and nonelectrolytes across membranes.

  5. Molecular Dynamics of a Water-Lipid Bilayer Interface

    Science.gov (United States)

    Wilson, Michael A.; Pohorille, Andrew

    1994-01-01

    We present results of molecular dynamics simulations of a glycerol 1-monooleate bilayer in water. The total length of analyzed trajectories is 5ns. The calculated width of the bilayer agrees well with the experimentally measured value. The interior of the membrane is in a highly disordered fluid state. Atomic density profile, orientational and conformational distribution functions, and order parameters indicate that disorder increases toward the center of the bilayer. Analysis of out-of-plane thermal fluctuations of the bilayer surfaces occurring at the time scale of the present calculations reveals that the distribution of modes agrees with predictions of the capillary wave model. Fluctuations of both bilayer surfaces are uncorrelated, yielding Gaussian distribution of instantaneous widths of the membrane. Fluctuations of the width produce transient thinning defects in the bilayer which occasionally span almost half of the membrane. The leading mechanism of these fluctuations is the orientational and conformational motion of head groups rather than vertical motion of the whole molecules. Water considerably penetrates the head group region of the bilayer but not its hydrocarbon core. The total net excess dipole moment of the interfacial water points toward the aqueous phase, but the water polarization profile is non-monotonic. Both water and head groups significantly contribute to the surface potential across the interface. The calculated sign of the surface potential is in agreement with that from experimental measurements, but the value is markedly overestimated. The structural and electrical properties of the water-bilayer system are discussed in relation to membrane functions, in particular transport of ions and nonelectrolytes across membranes.

  6. Static and dynamic contact angles of water droplet on a solid surface using molecular dynamics simulation.

    Science.gov (United States)

    Hong, Seung Do; Ha, Man Yeong; Balachandar, S

    2009-11-01

    The present study investigates the variation of static contact angle of a water droplet in equilibrium with a solid surface in the absence of a body force and the dynamic contact angles of water droplet moving on a solid surface for different characteristic energies using the molecular dynamics simulation. With increasing characteristic energy, the static contact angle in equilibrium with a solid surface in the absence of a body force decreases because the hydrophobic surface changes its characteristics to the hydrophilic surface. In order to consider the effect of moving water droplet on the dynamic contact angles, we apply the constant acceleration to an individual oxygen and hydrogen atom. In the presence of a body force, the water droplet changes its shape with larger advancing contact angle than the receding angle. The dynamic contact angles are compared with the static contact angle in order to see the effect of the presence of a body force.

  7. Dynamics of water and solute transport in polymeric reverse osmosis membranes via molecular dynamics simulations

    CERN Document Server

    Shen, Meng; Lueptow, Richard M

    2016-01-01

    The Angstrom-scale transport characteristics of water and six different solutes, methanol, ethanol, 2-propanol, urea, Na+, and Cl-, were studied for a polyamide reverse osmosis (RO) membrane, FT-30, using non-equilibrium molecular dynamics (NEMD) simulations. Results indicate that water transport increases with an increasing fraction of connected percolated free volume, or water-accessible open space, in the membrane polymer structure. This free volume is enhanced by the dynamic structure of the membrane at the molecular level as it swells when hydrated and vibrates due to molecular collisions allowing a continuous path connecting the opposite membrane surfaces. The tortuous paths available for transport of solutes result in Brownian motion of solute molecules and hopping from pore to pore as they pass through the polymer network structure of the membrane. The transport of alcohol solutes decreases for solutes with larger Van der Waals volume, which corresponds to less available percolated free volume, or sol...

  8. Dynamic Water Networks in Cytochrome c Oxidase from Paracoccus denitrificans Investigated by Molecular Dynamics Simulations

    OpenAIRE

    Olkhova, Elena; Hutter, Michael C; Lill, Markus A.; Helms, Volkhard; Michel, Hartmut

    2004-01-01

    We present a molecular dynamics study of cytochrome c oxidase from Paracoccus denitrificans in the fully oxidized state, embedded in a fully hydrated dimyristoylphosphatidylcholine lipid bilayer membrane. Parallel simulations with different levels of protein hydration, 1.125 ns each in length, were carried out under conditions of constant temperature and pressure using three-dimensional periodic boundary conditions and full electrostatics to investigate the distribution and dynamics of water ...

  9. Molecular dynamics simulation of liquid water confined inside graphite channels: dielectric and dynamical properties.

    Science.gov (United States)

    Martí, J; Nagy, G; Guàrdia, E; Gordillo, M C

    2006-11-30

    Electric and dielectric properties and microscopic dynamics of liquid water confined between graphite slabs are analyzed by means of molecular dynamics simulations for several graphite-graphite separations at ambient conditions. The electric potential across the interface shows oscillations due to water layering, and the overall potential drop is about -0.28 V. The total dielectric constant is larger than the corresponding value for the bulklike internal region of the system. This is mainly due to the preferential orientations of water nearest the graphite walls. Estimation of the capacitance of the system is reported, indicating large variations for the different adsorption layers. The main trend observed concerning water diffusion is 2-fold: on one hand, the overall diffusion of water is markedly smaller for the closest graphite-graphite separations, and on the other hand, water molecules diffuse in interfaces slightly slower than those in the bulklike internal areas. Molecular reorientational times are generally larger than those corresponding to those of unconstrained bulk water. The analysis of spectral densities revealed significant spectral shifts, compared to the bands in unconstrained water, in different frequency regions, and associated to confinement effects. These findings are important because of the scarce information available from experimental, theoretical, and computer simulation research into the dielectric and dynamical properties of confined water.

  10. Elucidating water dynamics in MgCl2 hydrates from molecular dynamics simulation

    Science.gov (United States)

    Huinink, Hendrik Pieter; Zahn, Dirk

    2017-07-01

    The water mobility in single crystals of MgCl2 hydrates has been investigated with molecular dynamics. Standard force fields have been benchmarked for molecular dynamics simulations of MgCl2 hydrates. To provide a reliable molecular mechanics model, force fields are selected on their ability to reproduce the structure of MgCl2·6H2O at 300 K. The selected force fields are then tested on their ability to also reproduce the structures of the different hydrates (n = 12, 8, 6, 4, 2, 1) and available thermodynamic data. For the currently best force-field available, constant-temperature, constant-pressure molecular dynamics simulations are preformed to elucidate the mechanisms of hydrate water mobility in perfect single crystals of the tetra- and hexahydrate. Long range water diffusion was not observed; each water molecule remained in the coordination sphere of its original Mg2+ host. However, collective ring-like motions of four water molecules at once within the coordination shell of a Magnesium ion were observed.

  11. Hydrogen bond dynamics in liquid water: Ab initio molecular dynamics simulation

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Cheolhee; Kim, Eunae [College of Pharmacy, Chosun University, Gwangju (Korea, Republic of); Yeom, Min Sun [Korea Institute of Science and Technology Information, Daejeon (Korea, Republic of)

    2016-01-15

    The effect of intermolecular interaction on the distribution of the harmonic vibrational frequencies of water molecules was investigated through ab initio molecular dynamics simulations based on the Born-Oppenheimer approach. For single water, the effect of the dynamics of the oxygen atom in single water and the simulation time step on the frequency distribution were examined. The distributions of the OH stretching and HOH bending vibrational frequencies of liquid water were compared to those of single water. The probability distributions of the change in OH bond length and the lifetime of the dangling OH bond were also obtained. The distribution of the frequencies was strongly affected by the long lifetime of the dangling OH bond, resulting in the formation of hydrogen bonds between water molecules.

  12. Molecular-dynamics of water transport through membranes - water from solvent to solute

    NARCIS (Netherlands)

    BERENDSEN, HJC; MARRINK, SJ

    1993-01-01

    An application of Molecular Dynamics computer simulation (MD) to the process of transport of water through a lipid bilayer membrane is described. The permeation process is far too slow to be modeled by straightforward MD. In stead the inverse of the permeability coefficient is expressed as an

  13. Vibrational spectrum at a water surface: a hybrid quantum mechanics/molecular mechanics molecular dynamics approach.

    Science.gov (United States)

    Ishiyama, Tatsuya; Takahashi, Hideaki; Morita, Akihiro

    2012-03-28

    A hybrid quantum mechanics/molecular mechanics (QM/MM) molecular dynamics (MD) simulation is applied to the calculation of surface orientational structure and vibrational spectrum (second-order nonlinear susceptibility) at the vapor/water interface for the first time. The surface orientational structure of the QM water molecules is consistent with the previous MD studies, and the calculated susceptibility reproduces the experimentally reported one, supporting the previous results using the classical force field MD simulation. The present QM/MM MD simulation also demonstrates that the positive sign of the imaginary part of the second-order nonlinear susceptibility at the lower hydrogen bonding OH frequency region originates not from individual molecular orientational structure, but from cooperative electronic structure through the hydrogen bonding network.

  14. Collective Molecular Dynamics of a Floating Water Bridge

    CERN Document Server

    Del Giudice, Emilio; Vitiello, Giuseppe

    2010-01-01

    When a high voltage is applied to pure water filling two beakers kept close to each other, a connection forms spontaneously, giving the impression of a floating water bridge. This phenomenon is of special interest, since it comprises a number of phenomena currently tackled in modern water science. The formation and the main properties of this floating water bridge are analyzed in the conceptual framework of quantum electrodynamics. The necessary conditions for the formation are investigated as well as the time evolution of the dynamics. The predictions are found in agreement with the observations.

  15. The interplay between dynamic heterogeneities and structure of bulk liquid water: A molecular dynamics simulation study.

    Science.gov (United States)

    Demontis, Pierfranco; Gulín-González, Jorge; Masia, Marco; Sant, Marco; Suffritti, Giuseppe B

    2015-06-28

    In order to study the interplay between dynamical heterogeneities and structural properties of bulk liquid water in the temperature range 130-350 K, thus including the supercooled regime, we use the explicit trend of the distribution functions of some molecular properties, namely, the rotational relaxation constants, the atomic mean-square displacements, the relaxation of the cross correlation functions between the linear and squared displacements of H and O atoms of each molecule, the tetrahedral order parameter q and, finally, the number of nearest neighbors (NNs) and of hydrogen bonds (HBs) per molecule. Two different potentials are considered: TIP4P-Ew and a model developed in this laboratory for the study of nanoconfined water. The results are similar for the dynamical properties, but are markedly different for the structural characteristics. In particular, for temperatures higher than that of the dynamic crossover between "fragile" (at higher temperatures) and "strong" (at lower temperatures) liquid behaviors detected around 207 K, the rotational relaxation of supercooled water appears to be remarkably homogeneous. However, the structural parameters (number of NNs and of HBs, as well as q) do not show homogeneous distributions, and these distributions are different for the two water models. Another dynamic crossover between "fragile" (at lower temperatures) and "strong" (at higher temperatures) liquid behaviors, corresponding to the one found experimentally at T(∗) ∼ 315 ± 5 K, was spotted at T(∗) ∼ 283 K and T(∗) ∼ 276 K for the TIP4P-Ew and the model developed in this laboratory, respectively. It was detected from the trend of Arrhenius plots of dynamic quantities and from the onset of a further heterogeneity in the rotational relaxation. To our best knowledge, it is the first time that this dynamical crossover is detected in computer simulations of bulk water. On the basis of the simulation results, the possible mechanisms of the two

  16. Molecular Dynamics Simulations of Water Droplets On Hydrophilic Silica Surfaces

    DEFF Research Database (Denmark)

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

    2009-01-01

    Wetting is essential and ubiquitous in a variety of natural and technological processes. Silicon dioxides-water systems are abundant in nature and play fundamental roles in a vast variety of novel science and engineering activities such as silicon based devices, nanoscale lab on a chip systems...... and DNA microarrays technologies.Although extensive experimental, theoretical and computational work has been devoted to study the nature of the interaction between silica and water, at the molecular level a complete understanding of silica-water systems has not been reached. Contact angle computations...

  17. Molecular Dynamics Simulations of Water Nanodroplets on Silica Surfaces

    DEFF Research Database (Denmark)

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

    2009-01-01

    Wetting is essential and ubiquitous in a variety of natural and technological processes.1,2,3 Silicon dioxides-water systems are abundant in nature and play fundamental roles in a vast variety of novel science and engineering activities such as silicon based devices, nanoscale lab on a chip systems...... and DNA microarrays technologies.4,5,6,7,8 Although extensive experimental, theoretical and computational work has been devoted to study the nature of the interaction between silica and water,2,9-16 at the molecular level a complete understanding of silica-water systems has not been reached. Contact angle...

  18. Molecular dynamics modeling of a nanomaterials-water surface interaction

    Science.gov (United States)

    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.

  19. Molecular dynamics

    Energy Technology Data Exchange (ETDEWEB)

    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.

  20. Solvation structures and dynamics of alkaline earth metal halides in supercritical water: A molecular dynamics study

    Science.gov (United States)

    Keshri, Sonanki; Mandal, Ratnamala; Tembe, B. L.

    2016-09-01

    Constrained molecular dynamics simulations of alkaline earth metal halides have been carried out to investigate their structural and dynamical properties in supercritical water. Potentials of mean force (PMFs) for all the alkaline earth metal halides in supercritical water have been computed. Contact ion pairs (CIPs) are found to be more stable than all other configurations of the ion pairs except for MgI2 where solvent shared ion pair (SShIP) is more stable than the CIP. There is hardly any difference in the PMFs between the M2+ (M = Mg, Ca, Sr, Ba) and the X- (X = F, Cl, Br, I) ions whether the second X- ion is present in the first coordination shell of the M2+ ion or not. The solvent molecules in the solvation shells diffuse at a much slower rate compared to the bulk. Orientational distribution functions of solvent molecules are sharper for smaller ions.

  1. Molecular dynamics simulation of water between two charged layers of dipalmitoylphosphatidylserine

    NARCIS (Netherlands)

    Cascales, J.J.L.; Berendsen, H.J.C.; delaTorre, J.G.

    1996-01-01

    A molecular dynamics simulation of water between two charged layers of dipalmitoylphosphatidylserine in its liquid-crystalline state with atomic detail was carried out. From an analysis of a trajectory of 184 ps of length, we obtained information about the dynamics and structure of water between suc

  2. Molecular dynamics

    NARCIS (Netherlands)

    Bergstra, J.A.; Bethke, I.

    2002-01-01

    Molecular dynamics is a model for the structure and meaning of object based programming systems. In molecular dynamics the memory state of a system is modeled as a fluid consisting of a collection of molecules. Each molecule is a collection of atoms with bindings between them. A computation is model

  3. The interplay between dynamic heterogeneities and structure of bulk liquid water: A molecular dynamics simulation study

    Energy Technology Data Exchange (ETDEWEB)

    Demontis, Pierfranco; Suffritti, Giuseppe B. [Dipartimento di Chimica e Farmacia, Università degli studi di Sassari, Sassari (Italy); Consorzio Interuniversitario Nazionale per la Scienza e Tecnologia dei Materiali (INSTM), Unità di ricerca di Sassari, Via Vienna, 2, I-07100 Sassari (Italy); Gulín-González, Jorge [Grupo de Matemática y Física Computacionales, Universidad de las Ciencias Informáticas (UCI), Carretera a San Antonio de los Baños, Km 21/2, La Lisa, La Habana (Cuba); Masia, Marco [Dipartimento di Chimica e Farmacia, Università degli studi di Sassari, Sassari (Italy); Consorzio Interuniversitario Nazionale per la Scienza e Tecnologia dei Materiali (INSTM), Unità di ricerca di Sassari, Via Vienna, 2, I-07100 Sassari (Italy); Istituto Officina dei Materiali del CNR, UOS SLACS, Via Vienna 2, 07100 Sassari (Italy); Sant, Marco [Dipartimento di Chimica e Farmacia, Università degli studi di Sassari, Sassari (Italy)

    2015-06-28

    In order to study the interplay between dynamical heterogeneities and structural properties of bulk liquid water in the temperature range 130–350 K, thus including the supercooled regime, we use the explicit trend of the distribution functions of some molecular properties, namely, the rotational relaxation constants, the atomic mean-square displacements, the relaxation of the cross correlation functions between the linear and squared displacements of H and O atoms of each molecule, the tetrahedral order parameter q and, finally, the number of nearest neighbors (NNs) and of hydrogen bonds (HBs) per molecule. Two different potentials are considered: TIP4P-Ew and a model developed in this laboratory for the study of nanoconfined water. The results are similar for the dynamical properties, but are markedly different for the structural characteristics. In particular, for temperatures higher than that of the dynamic crossover between “fragile” (at higher temperatures) and “strong” (at lower temperatures) liquid behaviors detected around 207 K, the rotational relaxation of supercooled water appears to be remarkably homogeneous. However, the structural parameters (number of NNs and of HBs, as well as q) do not show homogeneous distributions, and these distributions are different for the two water models. Another dynamic crossover between “fragile” (at lower temperatures) and “strong” (at higher temperatures) liquid behaviors, corresponding to the one found experimentally at T{sup ∗} ∼ 315 ± 5 K, was spotted at T{sup ∗} ∼ 283 K and T{sup ∗} ∼ 276 K for the TIP4P-Ew and the model developed in this laboratory, respectively. It was detected from the trend of Arrhenius plots of dynamic quantities and from the onset of a further heterogeneity in the rotational relaxation. To our best knowledge, it is the first time that this dynamical crossover is detected in computer simulations of bulk water. On the basis of the simulation results, the possible

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

    DEFF Research Database (Denmark)

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

    2010-01-01

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

  5. Molecular dynamics study of water and water/chlorinated hydrocargon mixtures with polarizable potential models

    Energy Technology Data Exchange (ETDEWEB)

    Dang, L.X. [Pacific Northwest National Lab., Richland, WA (United States)

    1997-12-31

    A series of molecular dynamics simulations were carried out to study water and water/chlorinated hydrocarbon mixtures. The properties of water clusters containing up to six water molecules were evaluated. A prism-like structure is predicted to be lowest in energy for the (H{sub 2}O){sub 6} cluster and a cage-like structure is the second lowest in energy with the energy about 0.2 kcal/mol higher than the prism-like structure. The computed dipole moments of water molecules in clusters indicated that there is a transition from cyclic planar configurations to three dimensional structure networks. The computed thermodynamic properties for the model including the liquid density, the enthalpy of vaporization, as well as the diffusion coefficient at room temperature, are in excellent agreement with experimental values. The computed density profile of the water of liquid/valor interface shows that the interface is not sharp at a microscopic level and has a thickness of 3.2 A at 298 K. The calculated surface tension at room temperature is in reasonably agreement with the corresponding experimental data. The computed average dipole moments of water molecules near the interface are close to their gas phase values. The thermodynamic and structural properties of water/chlorinated hydrocarbon mixtures as a function of mole fraction were evaluated.

  6. Self consistent tight binding molecular dynamics study of Ti02 nanoclusters in water.

    Energy Technology Data Exchange (ETDEWEB)

    Erdin, S.; Lin, Y.; Halley, J. W.; Zapol, P.; Redfern, P.; Curtiss, L.; Northern Illinois Univ.; Univ. of Minnesota

    2007-09-01

    Self-consistent tight binding molecular dynamics studies of TiO{sub 2}2 anatase and rutile nanoclusters in dissociable water are reported. It is found that the structure of the particle expands as a result of interaction between the particle's surface and water. Water molecules dissociate at the nanoparticle surface during simulation.

  7. Coupling all-atom molecular dynamics simulations of ions in water with Brownian dynamics

    CERN Document Server

    Erban, Radek

    2015-01-01

    Molecular dynamics (MD) simulations of ions (K$^+$, Na$^+$, Ca$^{2+}$ and Cl$^-$) in aqueous solutions are investigated. Water is described using the SPC/E model. A stochastic coarse-grained description for ion behaviour is presented and parameterized using MD simulations. It is given as a system of coupled stochastic and ordinary differential equations, describing the ion position, velocity and acceleration. The stochastic coarse-grained model provides an intermediate description between all-atom MD simulations and Brownian dynamics (BD) models. It is used to develop a multiscale method which uses all-atom MD simulations in parts of the computational domain and (less detailed) BD simulations in the remainder of the domain.

  8. Molecular dynamics simulation study of water adsorption on hydroxylated graphite surfaces.

    Science.gov (United States)

    Picaud, Sylvain; Collignon, B; Hoang, Paul N M; Rayez, J C

    2006-04-27

    In this paper, we present results from molecular dynamic simulations devoted to the characterization of the interaction between water molecules and hydroxylated graphite surfaces considered as models for surfaces of soot emitted by aircraft. The hydroxylated graphite surfaces are modeled by anchoring several OH groups on an infinite graphite plane. The molecular dynamics simulations are based on a classical potential issued from quantum chemical calculations. They are performed at three temperatures (100, 200, and 250 K) to provide a view of the structure and dynamics of water clusters on the model soot surface. These simulations show that the water-OH sites interaction is quite weak compared to the water-water interaction. This leads to the clustering of the water molecules above the surface, and the corresponding water aggregate can only be trapped by the OH sites when the temperature is sufficiently low, or when the density of OH sites is sufficiently high.

  9. Vibrational frequency fluctuations of ionic vibrational probe in water: Theoretical study with molecular dynamics simulation

    Science.gov (United States)

    Okuda, Masaki; Higashi, Masahiro; Ohta, Kaoru; Saito, Shinji; Tominaga, Keisuke

    2017-09-01

    The vibrational dynamics of SCN- in H2O are theoretically investigated by molecular dynamics simulations. Based on the vibrational solvatochromism theory, we calculate the frequency-frequency time correlation function of the SCN anti-symmetric stretching mode, which is characterized by time constants of 0.13 and 1.41 ps. We find that the frequency fluctuation is almost determined by the electrostatic interaction from the water molecules in the first-hydration shell. The collective dynamics of the water molecules in the first-hydration shell is found to be similar to that of bulk water, though the hydrogen bond between the ion and water molecule is very strong.

  10. Molecular properties of aqueous solutions: a focus on the collective dynamics of hydration water.

    Science.gov (United States)

    Comez, L; Paolantoni, M; Sassi, P; Corezzi, S; Morresi, A; Fioretto, D

    2016-07-07

    When a solute is dissolved in water, their mutual interactions determine the molecular properties of the solute on one hand, and the structure and dynamics of the surrounding water particles (the so-called hydration water) on the other. The very existence of soft matter and its peculiar properties are largely due to the wide variety of possible water-solute interactions. In this context, water is not an inert medium but rather an active component, and hydration water plays a crucial role in determining the structure, stability, dynamics, and function of matter. This review focuses on the collective dynamics of hydration water in terms of retardation with respect to the bulk, and of the number of molecules whose dynamics is perturbed. Since water environments are in a dynamic equilibrium, with molecules continuously exchanging from around the solute towards the bulk and vice versa, we examine the ability of different techniques to measure the water dynamics on the basis of the explored time scales and exchange rates. Special emphasis is given to the collective dynamics probed by extended depolarized light scattering and we discuss whether and to what extent the results obtained in aqueous solutions of small molecules can be extrapolated to the case of large biomacromolecules. In fact, recent experiments performed on solutions of increasing complexity clearly indicate that a reductionist approach is not adequate to describe their collective dynamics. We conclude this review by presenting current ideas that are being developed to describe the dynamics of water interacting with macromolecules.

  11. Isotope effects in water as investigated by neutron diffraction and path integral molecular dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Zeidler, Anita [University of Bath; Salmon, Phil [University of Bath; Fischer, Henry E [Institut Laue-Langevin (ILL); Neuefeind, Joerg C [ORNL; Simonson, J Michael {Mike} [ORNL; Markland, Thomas [Columbia University

    2012-01-01

    The structure of heavy and light water at 300 K was investigated by using a joint approach in which the method of neutron di raction with oxygen isotope substitution was combined with path integral molecular dynamics simulations. The di raction results, which give intra-molecular O-D and O-H bond distances of 0.985(5) and 0.990(5) A, were found to be in best agreement with those obtained by using the exible anharmonic TTM3-F water model. Both techniques show a di erence of '0.5% between the O-D and O-H intra-molecular bond lengths and the results support a competing quantum e ects model for water in which its structural and dynamical properties are governed by an o set between intra-molecular and inter-molecular quantum contributions. Further consideration of the O-O correlations is needed in order to improve agreement with experiment.

  12. Isotope effects in water as investigated by neutron diffraction and path integral molecular dynamics

    Science.gov (United States)

    Zeidler, Anita; Salmon, Philip S.; Fischer, Henry E.; Neuefeind, Jörg C.; Simonson, J. Mike; Markland, Thomas E.

    2012-07-01

    The structures of heavy and light water at 300 K were investigated by using a joint approach in which the method of neutron diffraction with oxygen isotope substitution was complemented by path integral molecular dynamics simulations. The diffraction results, which give intra-molecular O-D and O-H bond distances of 0.985(5) and 0.990(5) Å, were found to be in best agreement with those obtained by using the flexible anharmonic TTM3-F water model. Both techniques show a difference of ≃ 0.5% between the O-D and O-H intra-molecular bond lengths, and the results support a competing quantum effects model for water in which its structural and dynamical properties are governed by an offset between intra-molecular and inter-molecular quantum contributions. Further consideration of the O-O correlations is needed in order to improve agreement with experiment.

  13. Molecular Dynamics Simulation of Diffusion Coefficients of Oxygen, Nitrogen and Sodium Chloride in Supercritical Water

    Institute of Scientific and Technical Information of China (English)

    肖吉; 陆九芳; 陈健; 李以圭

    2001-01-01

    Molecular dynamics simulation has been performed to determine the infinite-dilution diffusion coefficients of oxygen and nitrogen, and the diffusion coefficients of NaCl in supercritical water from 703.2- 763.2 K and 30-45 MPa.The results obtained show that the diffusion coefficients in supercritical water increase with temperature, while decreasing with pressure. Nevertheless, the diffusion coefficients in supercritical water are much larger than those in normal water.

  14. Hydrogen bonding and related properties in liquid water: a Car-Parrinello molecular dynamics simulation study

    OpenAIRE

    Guàrdia Manuel, Elvira; Skarmoutsos, Ioannis; Masia, Marco

    2015-01-01

    The local hydrogen-bonding structure and dynamics of liquid water have been investigated using the Car-Parrinello molecular dynamics simulation technique. The radial distribution functions and coordination numbers around water molecules have been found to be strongly dependent on the number of hydrogen bonds formed by each molecule, revealing also the existence of local structural heterogeneities in the structure of the liquid. The results obtained have also revealed the strong effect of the ...

  15. Molecular Dynamics Simulation on Charge Transfer Relaxation between Myoglobin and Water

    Institute of Scientific and Technical Information of China (English)

    CHENG Wei; ZHANG Feng-Shou; ZHANG Bo-Yang; ZHOU Hong-Yu

    2007-01-01

    Dynamical processes of myoglobin after photon-excited charge transfer between Fe ion and surrounding water anion ale simulated by a molecular dynamics model.The roles of Coulomb interaction effect and water effect in the relaxation process are discussed.It is found that the relaxations before and after charge transfer are similar.Strong Coulomb interactions and less water mobility decrease Coulomb energy fluctuations.An extra transferred charge of Fe ion has impact on water packing with a distance up to 0.86nm.

  16. Molecular Dynamics Simulation of a Membrane/Water Interface : The Ordering of Water and Its Relation to the Hydration Force

    NARCIS (Netherlands)

    Marrink, Siewert-Jan; Berkowitz, Max; Berendsen, Herman J.C.

    1993-01-01

    In order to obtain a better understanding of the origin of the hydration force, three molecular dynamic simulations of phospholipid/water multilamellar systems were performed. The simulated systems only differed in the amount of interbilayer water, ranging from the minimum to the maximum amount of

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

    KAUST Repository

    Yoon, Seyoon

    2013-01-01

    The molecular structure and dynamics of interlayer water of 14 Å tobermorite are investigated based on molecular dynamics (MD) simulations. Calculated structural parameters of the interlayer water configuration are in good agreement with current knowledge of the refined structure. The MD simulations provide detailed information on the position and mobility of the hydrogen and oxygen of interlayer water, as well as its self-diffusion coefficient, through the interlayer of 14 Å tobermorite. Comparison of the MD simulation results at 100 and 300 K demonstrates that water molecules in the interlayer maintain their structure but change their mobility. The dominant configuration and self-diffusion coefficient of interlayer water are obtained in this study. Copyright © 2013 Japan Concrete Institute.

  18. Understanding flocculation mechanism of graphene oxide for organic dyes from water: Experimental and molecular dynamics simulation

    Science.gov (United States)

    Liu, Jun; Li, Peng; Xiao, Hang; Zhang, Yayun; Shi, Xiaoyang; Lü, Xiaomeng; Chen, Xi

    2015-11-01

    Flocculation treatment processes play an important role in water and wastewater pretreatment. Here we investigate experimentally and theoretically the possibility of using graphene oxide (GO) as a flocculant to remove methylene blue (MB) from water. Experimental results show that GO can remove almost all MB from aqueous solutions at its optimal dosages and molecular dynamics simulations indicate that MB cations quickly congregate around GO in water. Furthermore, PIXEL energy contribution analysis reveals that most of the strong interactions between GO and MB are of a van der Waals (London dispersion) character. These results offer new insights for shedding light on the molecular mechanism of interaction between GO and organic pollutants.

  19. Interaction of monovalent ions with the water liquid-vapor interface - A molecular dynamics study

    Science.gov (United States)

    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.

  20. Understanding flocculation mechanism of graphene oxide for organic dyes from water: Experimental and molecular dynamics simulation

    Directory of Open Access Journals (Sweden)

    Jun Liu

    2015-11-01

    Full Text Available Flocculation treatment processes play an important role in water and wastewater pretreatment. Here we investigate experimentally and theoretically the possibility of using graphene oxide (GO as a flocculant to remove methylene blue (MB from water. Experimental results show that GO can remove almost all MB from aqueous solutions at its optimal dosages and molecular dynamics simulations indicate that MB cations quickly congregate around GO in water. Furthermore, PIXEL energy contribution analysis reveals that most of the strong interactions between GO and MB are of a van der Waals (London dispersion character. These results offer new insights for shedding light on the molecular mechanism of interaction between GO and organic pollutants.

  1. Interaction of monovalent ions with the water liquid-vapor interface - A molecular dynamics study

    Science.gov (United States)

    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.

  2. Hydration of methanol in water. A DFT-based molecular dynamics study

    CERN Document Server

    Van Erp, T S; Erp, Titus S. van; Meijer, Evert Jan

    2000-01-01

    We studied the hydration of a single methanol molecule in aqueous solution by first-principle DFT-based molecular dynamics simulation. The calculations show that the local structural and short-time dynamical properties of the water molecules remain almost unchanged by the presence of the methanol, confirming the observation from recent experimental structural data for dilute solutions. We also see, in accordance with this experimental work, a distinct shell of water molecules that consists of about 15 molecules. We found no evidence for a strong tangential ordering of the water molecules in the first hydration shell.

  3. Molecular dynamics simulation of adsorption of an oil-water-surfactant mixture on calcite surface

    Institute of Scientific and Technical Information of China (English)

    Lu Guiwu; Zhang Xuefen; Shao Changjin; Yang Hong

    2009-01-01

    An interface super molecular structure model for oil-water-surfactant mixture and calcite was established. By using a molecular dynamics method, the effects of rhamnolipid, sodium dodecyl benzene sulfonate and sodium hexadecyl sulfonate on the interface adsorption behavior of oil molecules were investigated. It was found that these three surfactants could reduce oil-calcite interface binding energy, and play a role of oil-displacing agent.

  4. Water dynamics: relation between hydrogen bond bifurcations, molecular jumps, local density & hydrophobicity.

    Science.gov (United States)

    Titantah, John Tatini; Karttunen, Mikko

    2013-10-21

    Structure and dynamics of water remain a challenge. Resolving the properties of hydrogen bonding lies at the heart of this puzzle. We employ ab initio Molecular Dynamics (AIMD) simulations over a wide temperature range. The total simulation time was ≈ 2 ns. Both bulk water and water in the presence of a small hydrophobic molecule were simulated. We show that large-angle jumps and bond bifurcations are fundamental properties of water dynamics and that they are intimately coupled to both local density and hydrogen bond strength oscillations in scales from about 60 to a few hundred femtoseconds: Local density differences are the driving force for bond bifurcations and the consequent large-angle jumps. The jumps are intimately connected to the recently predicted hydrogen bond energy asymmetry. Our analysis also appears to confirm the existence of the so-called negativity track provided by the lone pairs of electrons on the oxygen atom to enable water rotation.

  5. Partition Coefficients of Organic Molecules in Squalane and Water/Ethanol Mixtures by Molecular Dynamics Simulations

    DEFF Research Database (Denmark)

    Lundsgaard, Rasmus; Kontogeorgis, Georgios; Economou, Ioannis G.

    2011-01-01

    coefficient can be estimated for both a small hydrophilic and a hydrophobic organic molecules between squalane (used here to mimic low density poly ethylene) and water/ethanol solutes using thermodynamic integration to calculate the free energy of solvation. Molecular dynamics simulations are performed, using...

  6. Molecular Dynamics Simulations of Water Droplets On Hydrophilic Silica Surfaces

    DEFF Research Database (Denmark)

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

    2009-01-01

    Wetting is essential and ubiquitous in a variety of natural and technological processes. Silicon dioxides-water systems are abundant in nature and play fundamental roles in a vast variety of novel science and engineering activities such as silicon based devices, nanoscale lab on a chip systems an...

  7. Structured Ionomer Thin Films at Water Interface: Molecular Dynamics Simulation Insight.

    Science.gov (United States)

    Aryal, Dipak; Agrawal, Anupriya; Perahia, Dvora; Grest, Gary S

    2017-09-08

    Controlling the structure and dynamics of thin films of ionizable polymers at water interfaces is critical to their many applications. As the chemical diversity within one polymer is increased, controlling the structure and dynamics of the polymer, which is a key to their use, becomes a challenge. Here molecular dynamics simulations (MD) are used to obtain molecular insight into the structure and dynamics of thin films of one such macromolecule at the interface with water. The polymer consists of an ABCBA topology with randomly sulfonated polystyrene (C), tethered symmetrically to flexible poly(ethylene-r-propylene) blocks (B), and end-capped by a poly(t-butylstyrene) block (A). The compositions of the interfacial and bulk regions of thin films of the ABCBA polymers are followed as a function of exposure time to water. We find that interfacial rearrangements take place where buried ionic segments migrate toward the water interface. The hydrophobic blocks collapse and rearrange to minimize their exposure to water. The water that initially drives interfacial reengagements breaks the ionic clusters within the film, forming a dynamic hydrophilic internal network within the hydrophobic segments.

  8. The Importance of Three-Body Interactions in Molecular Dynamics Simulations of Water with the Fragment Molecular Orbital Method

    Energy Technology Data Exchange (ETDEWEB)

    Pruitt, Spencer R.; Nakata, Hiroya; Nagata, Takeshi; Mayes, Maricris; Alexeev, Yuri; Fletcher, Graham D.; Fedorov, Dmitri G; Kitaura, Kazuo; Gordon, M

    2016-04-12

    The analytic first derivative with respect to nuclear coordinates is formulated and implemented in the framework of the three-body fragment molecular orbital (FMO) method. The gradient has been derived and implemented for restricted Hartree-Fock, second-order Møller-Plesset perturbation, and density functional theories. The importance of the three-body fully analytic gradient is illustrated through the failure of the two-body FMO method during molecular dynamics simulations of a small water cluster. The parallel implementation of the fragment molecular orbital method, its parallel efficiency, and its scalability on the Blue Gene/Q architecture up to 262,144 CPU cores, are also discussed.

  9. Isobaric first-principles molecular dynamics of liquid water with nonlocal van der Waals interactions

    CERN Document Server

    Miceli, Giacomo; Pasquarello, Alfredo

    2016-01-01

    We investigate the structural properties of liquid water at near ambient conditions using first-principles molecular dynamics simulations based on a semilocal density functional augmented with nonlocal van der Waals interactions. The adopted scheme offers the advantage of simulating liquid water at essentially the same computational cost of standard semilocal functionals. Applied to the water dimer and to ice Ih, we find that the hydrogen-bond energy is only slightly enhanced compared to a standard semilocal functional. We simulate liquid water through molecular dynamics in the NpH statistical ensemble allowing for fluctuations of the system density. The structure of the liquid departs from that found with a semilocal functional leading to more compact structural arrangements. This indicates that the directionality of the hydrogen-bond interaction has a diminished role as compared to the overall attractions, as expected when dispersion interactions are accounted for. This is substantiated through a detailed a...

  10. Molecular Dynamics Simulation of Water Nanodroplets on Silica Surfaces at High Air Pressures

    DEFF Research Database (Denmark)

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

    2010-01-01

    e.g., nanobubbles. In the present work we study the role of air on the wetting of hydrophilic systems. We conduct molecular dynamics simulations of a water nanodroplet on an amorphous silica surface at different air pressures. The interaction potentials describing the silica, water, and air...... are obtained from the literature. The silica surface is modeled by a large 32 ⨯ 32 ⨯ 2 nm amorphous SiO2 structure consisting of 180000 atoms. The water consists of 18000 water molecules surrounded by N2 and O2 air molecules corresponding to air pressures of 0 bar (vacuum), 50 bar, 100 bar and 200 bar. We...... perform extensive simulations of the water- air equilibrium and calibrate the water-air interaction to match the experimental solubility of N2 and O2 in water. For the silica-water system we calibrate the water-silica interaction to match the experimental contact angle of 27º. We subsequently study...

  11. Molecular Dynamical Simulation of Water/Ice Phase Transitions within Carbon Nanotubes under Various Pressures

    Institute of Scientific and Technical Information of China (English)

    YIN Bing; DONG Shun-Le

    2009-01-01

    A molecular dynamics simulation is performed for water confined within carbon nanotubes with diameters 11.00 (A) and 12.38 (A).Under pressures from 0.1 MPa to 500MPa the simulations are carried out by cooling from 300K to 240 K.Water molecules tend to transform from disordered to ordered with different configurations (square,pentagonal,hexagonal and hexagonal plus a chain).It is concluded that denser structures may appear under high pressures.

  12. Molecular Dynamics Simulations of the Solubility of H2S and CO2 in Water

    OpenAIRE

    Roberto López Rendón; José Alejandre

    2008-01-01

    We have performed molecular dynamics simulations at constant temperature and pressure to calculate the solubility of carbon dioxide (CO2) and hydrogen sulfide (H2S) in water. The solubility of gases in water is important in several technological problems, in particular in the petroleum industry. The calculated liquid densities as function of temperature are in good agreement with experimental data. The results at the liquid-vapor equilibrium show that at low temperatures there is an important...

  13. Development of EEM based silicon-water and silica-water wall potentials for non-reactive molecular dynamics simulations

    Science.gov (United States)

    Kim, Junghan; Iype, Eldhose; Frijns, Arjan J. H.; Nedea, Silvia V.; van Steenhoven, Anton A.

    2014-07-01

    Molecular dynamics simulations of heat transfer in gases are computationally expensive when the wall molecules are explicitly modeled. To save computational time, an implicit boundary function is often used. Steele's potential has been used in studies of fluid-solid interface for a long time. In this work, the conceptual idea of Steele's potential was extended in order to simulate water-silicon and water-silica interfaces. A new wall potential model is developed by using the electronegativity-equalization method (EEM), a ReaxFF empirical force field and a non-reactive molecular dynamics package PumMa. Contact angle simulations were performed in order to validate the wall potential model. Contact angle simulations with the resulting tabulated wall potentials gave a silicon-water contact angle of 129°, a quartz-water contact angle of 0°, and a cristobalite-water contact angle of 40°, which are in reasonable agreement with experimental values.

  14. Molecular dynamics studies of pathways of water movement in cyanobacterial photosystem II

    Energy Technology Data Exchange (ETDEWEB)

    Gabdulkhakov, A. G., E-mail: azat@vega.protres.ru; Kljashtorny, V. G.; Dontsova, M. V. [Russian Academy of Sciences, Institute of Protein Research (Russian Federation)

    2015-01-15

    Photosystem II (PSII) catalyzes the light-induced generation of oxygen from water. The oxygen-evolving complex is buried deep in the protein on the lumenal side of PSII, and water molecules need to pass through protein subunits to reach the active site—the manganese cluster. Previous studies on the elucidation of water channels in PSII were based on an analysis of the cavities in the static PSII structure determined by X-ray diffraction. In the present study, we perform molecular dynamics simulations of the water movement in the transport system of PSII.

  15. The hydrophobic effect: Molecular dynamics simulations of water confined between extended hydrophobic and hydrophilic surfaces

    DEFF Research Database (Denmark)

    Jensen, Morten Østergaard; Mouritsen, Ole G.; Peters, Günther H.J.

    2004-01-01

    experimental data from x-ray reflectivity measurements, reveal a uniform weak de-wetting characteristic for the extended hydrophobic surface, while the hydrophilic surface is weakly wetted. These microscopic data are consistent with macroscopic contact angle measurements. Specific water orientation is present......-correlation functions reveal that water molecules have characteristic diffusive behavior and orientational ordering due to the lack of hydrogen bonding interactions with the surface. These observations suggest that the altered dynamical properties of water in contact with extended hydrophobic surfaces together......Structural and dynamic properties of water confined between two parallel, extended, either hydrophobic or hydrophilic crystalline surfaces of n-alkane C36H74 or n-alcohol C35H71OH, are studied by molecular dynamics simulations. Electron density profiles, directly compared with corresponding...

  16. Molecular Dynamics Simulations of a Flexible Polyethylene: A Protein-Like Behaviour in a Water Solvent

    CERN Document Server

    Kretov, D A

    2005-01-01

    We used molecular dynamics (MD) simulations to study the density and the temperature behaviour of a flexible polyethylene (PE) subjected to various heating conditions and to investigate the PE chain conformational changes in a water solvent. First, we have considered the influence of the heating process on the final state of the polymeric system and the sensitivity of its thermodynamic characteristics (density, energy, etc.) for different heating regimes. For this purpose three different simulations were performed: fast, moderate, and slow heating. Second, we have investigated the PE chain conformational dynamics in water solvent for various simulation conditions and various configurations of the environment. From the obtained results we have got the pictures of the PE dynamical motions in water. We have observed a protein-like behaviour of the PE chain, like that of the DNA and the proteins in water, and have also estimated the rates of the conformational changes. For the MD simulations we used the optimized...

  17. Molecular Dynamics Simulation of Water Pore Formation in Lipid Bilayer Induced by Shock Waves

    Science.gov (United States)

    Koshiyama, Ken-ichiro; Kodama, Tetsuya; Yano, Takeru; Fujikawa, Shigeo

    2006-05-01

    Water molecule penetration into a bilayer hydrophobic region with a shock wave impulse has been investigated using molecular dynamics simulations [Koshiyama et al., AIP Conference Proceedings, 754, 104-106, (2005)]. Here we report results of simulation of spontaneous water pore formation in a bilayer that contains water molecules in the hydrophobic region in an initial state. The bilayers of 128 DPPC lipid and 3655 water molecules with insertion of 392, 784, and 1176 water molecules in the hydrophobic region are simulated. A water pore is spontaneously formed when 1176 water molecules exist in the hydrophobic region. The water pore diameter is estimated to be c.a. 1.9 nm, which is three times larger than that of 5-fluorouracil (5FU) used in cancer treatment.

  18. Dynamics of biological water: insights from molecular modeling of light scattering in aqueous trehalose solutions.

    Science.gov (United States)

    Lupi, Laura; Comez, Lucia; Paolantoni, Marco; Fioretto, Daniele; Ladanyi, Branka M

    2012-06-28

    Extended depolarized light scattering (EDLS) measurements have been recently employed to investigate the dynamics of water solvating biological molecules, giving evidence of the presence of two different dynamical regimes among water molecules. An interpretation of EDLS has been proposed that provides an independent estimate of the retardation factor of slowdown with respect to fast water molecules and of the number of solvent molecules affected by this slowing down. Nevertheless this measure is an inherently complex one, due to the collective nature of the physical property probed. In the present work a molecular dynamics (MD) approach has been used to more deeply understand experimental results. Time correlation functions of the collective polarizability anisotropy have been calculated for the prototype disaccharide trehalose in aqueous solutions as a function of concentration. The unique capability of MD to disentangle the contributions to the dynamics arising from solute, solvent, and cross terms between the two allowed us to check the reliability of an interpretation that assumes a spectral separation of water and sugar dynamics, as well as to highlight the very presence of two distinct relaxation processes in water. The two processes have been attributed to the dynamics of bulk and hydration water, respectively. A retardation factor of ~5 and concentration dependent hydration numbers have been observed, in good agreement with experimental results [Paolantoni, M.; et al. J. Phys. Chem. B 2009, 113, 7874-7878].

  19. Water hexamer: Self-consistent phonons versus reversible scaling versus replica exchange molecular dynamics

    CERN Document Server

    Brown, Sandra E

    2014-01-01

    Classical free energies for the cage and prism isomers of water hexamer computed by the self- consistent phonons (SCP) method and reversible scaling (RS) method are presented for several flexible water potentials. Both methods have been augmented with a rotational correction for improved accuracy when working with clusters. Comparison of the SCP results with the RS results suggests a fairly broad temperature range over which the SCP approximation can be expected to give accurate results for systems of water clusters, and complements a previously reported assessment of SCP. Discrepancies between the SCP and RS results presented here, and recently published replica exchange molecular dynamics (REMD) results bring into question the convergence of the REMD and accompanying replica exchange path integral molecular dynamics results. In addition to the ever-present specter of unconverged results, several possible sources for the discrepancy are explored based on inherent characteristics of the methods used.

  20. Molecular dynamics simulation of nanosized water droplet spreading in an electric field.

    Science.gov (United States)

    Song, F H; Li, B Q; Liu, C

    2013-04-02

    Molecular dynamics (MD) simulations are performed for the spreading of a nanosized water droplet on a solid substrate subject to a parallel electric field. A combined electrostatic and Lennard-Jones potential is employed to represent the intermolecular interactions. Results show that in response to the applied field, polar water molecules realign themselves and this microscopic reorientation of molecular dipoles combines with the intermolecular forces to produce a macroscopic deformation of a free spherical water droplet into an ellipsoid. The applied field has a strong effect on the spreading of the water droplet on a solid substrate. For a weaker parallel field, the droplet spreading is asymmetric with the leading contact angle being greater than the trailing contact angle. With an increase in field strength, this asymmetry continues to increase, culminates, and then decreases until it disappears. The symmetric spreading remains with a further increase in the field strength until the saturation point is reached. This transition from the asymmetric to symmetric spreading is a manifestation of the interaction of the electric field with polar water molecules and the intermolecular forces within the droplet and between the water and solid; the interaction also leads to a change in hydrogen bonds along the droplet surface. The dynamics of the droplet spreading is entailed by the electrically induced motion of molecules along the liquid surface toward the solid substrate and is controlled by a competing mechanism among the electric, water-water, and water-solid intermolecular forces.

  1. Molecular dynamics simulation of the behaviour of water in nano-confined ionic liquid-water mixtures

    Science.gov (United States)

    Docampo-Álvarez, B.; Gómez-González, V.; Montes-Campos, H.; Otero-Mato, J. M.; Méndez-Morales, T.; Cabeza, O.; Gallego, L. J.; Lynden-Bell, R. M.; Ivaništšev, V. B.; Fedorov, M. V.; Varela, L. M.

    2016-11-01

    This work describes the behaviour of water molecules in 1-butyl-3-methylimidazolium tetrafluoroborate ionic liquid under nanoconfinement, between graphene sheets. By means of molecular dynamics simulations, the adsorption of water molecules at the graphene surface is studied. A depletion of water molecules in the vicinity of the neutral and negatively charged graphene surfaces, and their adsorption at the positively charged surface are observed in line with the preferential hydration of the ionic liquid anions. The findings are appropriately described using a two-level statistical model. The confinement effect on the structure and dynamics of the mixtures is thoroughly analyzed using the density and the potential of mean force profiles, as well as by the vibrational densities of the states of water molecules near the graphene surface. The orientation of water molecules and the water-induced structural transitions in the layer closest to the graphene surface are also discussed.

  2. Polarizability effects in molecular dynamics simulations of the graphene-water interface

    Science.gov (United States)

    Ho, Tuan A.; Striolo, Alberto

    2013-02-01

    The importance of including the polarizability of both water and graphene in molecular dynamics simulations of the water/graphene system was quantified. A thin film of either rigid single point charge extended (SPC/E) water or polarizable simple 4-site water model with Drude polarizability (SWM4_DP) water on non-polarizable and polarizable graphene surfaces was simulated. The graphene surface was either maintained neutral or charged, positively and negatively. The results suggest that SPC/E and SWM4_DP water models yield very similar predictions for the water structural properties on neutral non-polarizable graphene, although they yield slightly different dynamical properties of interfacial water on neutral non-polarizable graphene. More pronounced were the differences obtained when graphene was modeled with a polarizable force field. In particular, the polarizability of graphene was found to enhance the number of interfacial SWM4_DP water molecules pointing one of their OH bonds towards the neutral surface. Despite this structural difference, the dynamical properties predicted for the interfacial SWM4_DP water were found to be independent on polarizability as long as the polarizability of a carbon atom is smaller than α = 0.878 Å. On charged graphene surfaces, the effect of polarizability of graphene on structural properties and some dynamical properties of SWM4_DP water is negligible because electrostatic forces due to surface charge dominate polarization forces, as expected. For all cases, our results suggest that the hydrogen bond network is insensitive to the polarizability of both water and graphene. Understanding how these effects will determine the accumulation of ions near neutral or charged graphene could have important implications for applications in the fields of energy storage and water desalination.

  3. Molecular Dynamics Studies of Structure and Functions of Water-Membrane Interfaces

    Science.gov (United States)

    Pohorille, Andrew; Wilson, Michael A.; DeVincenzi, Donald L. (Technical Monitor)

    2001-01-01

    A large number of essential cellular processes occur at the interfaces between water and membranes. The selectivity and dynamics of these processes are largely determined by the structural and electrical properties of the water-membrane interface. We investigate these properties by the molecular dynamics method. Over the time scales of the simulations, the membrane undergoes fluctuations described by the capillary wave model. These fluctuations produce occasional thinning defects in the membrane which provide effective pathways for passive transport of ions and small molecules across the membrane. Ions moving through the membrane markedly disrupt its structure and allow for significant water penetration into the membrane interior. Selectivity of transport, with respect to ionic charge, is determined by the interfacial electrostatic potential. Many small molecules. of potential significance in catalysis, bioenergetics and pharmacology, are shown to bind to the interface. The energetics and dynamics of this process will be discussed.

  4. Molecular Dynamics Studies of Structure and Functions of Water-Membrane Interfaces

    Science.gov (United States)

    Pohorille, Andrew; Wilson, Michael A.; DeVincenzi, Donald L. (Technical Monitor)

    2001-01-01

    A large number of essential cellular processes occur at the interfaces between water and membranes. The selectivity and dynamics of these processes are largely determined by the structural and electrical properties of the water-membrane interface. We investigate these properties by the molecular dynamics method. Over the time scales of the simulations, the membrane undergoes fluctuations described by the capillary wave model. These fluctuations produce occasional thinning defects in the membrane which provide effective pathways for passive transport of ions and small molecules across the membrane. Ions moving through the membrane markedly disrupt its structure and allow for significant water penetration into the membrane interior. Selectivity of transport, with respect to ionic charge, is determined by the interfacial electrostatic potential. Many small molecules. of potential significance in catalysis, bioenergetics and pharmacology, are shown to bind to the interface. The energetics and dynamics of this process will be discussed.

  5. Enhanced heating of salty water and ice under microwaves: Molecular dynamics study

    OpenAIRE

    Tanaka, Motohiko; Sato, Motoyasu

    2008-01-01

    By molecular dynamics simulations, we have studied the enhanced heating process of salty ice and water by the electric field of applied microwaves at 2.5 GHz, and those in the range 2.5-10 GHz for the frequency dependence. We show that water molecules in salty ice are allowed to rotate in response to the microwave electric field to the extent comparable to those in pure water, because the molecules in salty ice are loosely tied by hydrogen bonds with adjacent molecules unlike the case of rigi...

  6. The Silica-Water Interface from the Analysis of Molecular Dynamic Simulations

    KAUST Repository

    Lardhi, Sheikha F.

    2013-05-01

    Surface chemistry is an emerging field that can give detailed insight about the elec- tronic properties and the interaction of complex material surfaces with their neigh- bors. This is for both solid-solid and solid-liquid interfaces. Among the latter class, the silica-water interface plays a major role in nature. Silica is among the most abundant materials on earth, as well in advanced technological applications such as catalysis and nanotechnology. This immediately indicates the relevance of a detailed understanding of the silica-water interface. In this study, we investigate the details of this interaction at microscopic level by analyzing trajectories obtained with ab initio molecular dynamic simulations. The system we consider consists of bulk liquid water confined between two β-cristobalite silica surfaces. The molecular dynamics were generated with the CP2K, an ab initio molecular dynamic simulation tool. The simulations are 25 picoseconds long, and the CP2K program was run on 64 cores on a supercomputer cluster. During the simulations the program integrates Newton’s equations of motion for the system and generates the trajectory for analysis. For analysis, we focused on the following properties that characterize the silica water interface. We calculated the density profile of the water layers from the silica surface, and we also calculated the radial distribution function (RDF) of the hydrogen bond at the silanols on the silica surface. The main focus of this thesis is to write the programs for calculating the atom density profile and the RDF from the generated MD trajectories. The atomic probability density profile shows that water is strongly adsorbed on the (001) cristobalite surface, while the RDF indicates differently ad- sorbed water molecules in the first adsorption layer. As final remark, the protocol and the tools developed in this thesis can be applied to the study of basically any crystal-water interface.

  7. Molecular-dynamic studies of carbon-water-carbon composite nanotubes.

    Science.gov (United States)

    Zou, Jian; Ji, Baohua; Feng, Xi-Qiao; Gao, Huajian

    2006-11-01

    We recently reported the discovery via molecular-dynamic simulations that single-walled carbon nanotubes (SWCNTs) with different diameters, lengths, and chiralities can coaxially self-assemble into multi-walled carbon nanotubes (MWCNTs) in water via the spontaneous insertion of smaller tubes into larger ones. Here, we extend that study to investigate the various water structures formed between two selected SWCNTs after such coaxial assembly. Depending on the tube geometry, typical water structures, besides the bulk phase, include a one-dimensional (1D) ordered water chain inside the smaller tube, a uniform or nonuniform water shell between the two tubes, and a "boundary layer" of water near the exterior wall of the larger tube. It was found that a concentric water shell consisting of up to three layers of water molecules can form between the two SWCNTs, which leads to a class of carbon-water-carbon composite nanotubes. Analysis of the potential energy of the SWCNT-water system indicated that the composite nanotubes are stabilized by both the tube-tube and tube-water van der Waals interactions. Geometrically confined between the two SWCNTs, water mono- and bilayers are found to be stable, highly condensed, and ordered, although the average number of hydrogen bonds per water molecule is reduced. In contrast, a water trilayer between the two CNTs can be easily disrupted by thermal fluctuations.

  8. A molecular dynamics study of the role of molecular water on the structure and mechanics of amorphous geopolymer binders

    Science.gov (United States)

    Sadat, Mohammad Rafat; Bringuier, Stefan; Asaduzzaman, Abu; Muralidharan, Krishna; Zhang, Lianyang

    2016-10-01

    In this paper, molecular dynamics simulations are used to study the effect of molecular water and composition (Si/Al ratio) on the structure and mechanical properties of fully polymerized amorphous sodium aluminosilicate geopolymer binders. The X-ray pair distribution function for the simulated geopolymer binder phase showed good agreement with the experimentally determined structure in terms of bond lengths of the various atomic pairs. The elastic constants and ultimate tensile strength of the geopolymer binders were calculated as a function of water content and Si/Al ratio; while increasing the Si/Al ratio from one to three led to an increase in the respective values of the elastic stiffness and tensile strength, for a given Si/Al ratio, increasing the water content decreased the stiffness and strength of the binder phase. An atomic-scale analysis showed a direct correlation between water content and diffusion of alkali ions, resulting in the weakening of the AlO4 tetrahedral structure due to the migration of charge balancing alkali ions away from the tetrahedra, ultimately leading to failure. In the presence of water molecules, the diffusion behavior of alkali cations was found to be particularly anomalous, showing dynamic heterogeneity. This paper, for the first time, proves the efficacy of atomistic simulations for understanding the effect of water in geopolymer binders and can thus serve as a useful design tool for optimizing composition of geopolymers with improved mechanical properties.

  9. Water on titanium dioxide surface: a revisiting by reactive molecular dynamics simulations.

    Science.gov (United States)

    Huang, Liangliang; Gubbins, Keith E; Li, Licheng; Lu, Xiaohua

    2014-12-16

    The behavior of surface water, especially the adsorption and dissociation characteristics, is a key to understanding and promoting photocatalytic and biomedical applications of titanium dioxide materials. Using molecular dynamics simulations with the ReaxFF force field, we study the interactions between water and five different TiO2 surfaces that are of interest to both experiments and theoretical calculations. The results show that TiO2 surfaces demonstrate different reactivities for water dissociation [rutile (011) > TiO2-B (100) > anatase (001) > rutile (110)], and there is no water dissociation observed on the TiO2-B (001) surface. The simulations also reveal that the water dissociation and the TiO2 surface chemistry change, and the new surface Ti-OH and O-H functional groups affect the orientation of other near-surface water molecules. On the reactive surface, such as the rutile (110) surface, water dissociated and formed new Ti-OH and O-H bonds on the surface. Those functional groups enhanced the hydrogen bond networking with the near-surface water molecules and their configurations. On the nonreactive TiO2-B (001) surface where no molecular or dissociative water adsorption is observed, near-surface water can also form hydrogen bonds with surface oxygen atoms of TiO2, but their distance to the surface is longer than that on the rutile (011) surface.

  10. Hydrogen bonding and vibrational energy relaxation of interfacial water: A full DFT molecular dynamics simulation.

    Science.gov (United States)

    Jeon, Jonggu; Hsieh, Cho-Shuen; Nagata, Yuki; Bonn, Mischa; Cho, Minhaeng

    2017-07-28

    The air-water interface has been a subject of extensive theoretical and experimental studies due to its ubiquity in nature and its importance as a model system for aqueous hydrophobic interfaces. We report on the structure and vibrational energy transfer dynamics of this interfacial water system studied with equilibrium and non-equilibrium molecular dynamics simulations employing a density functional theory -based description of the system and the kinetic energy spectral density analysis. The interfacial water molecules are found to make fewer and weaker hydrogen (H)-bonds on average compared to those in the bulk. We also find that (i) the H-bonded OH groups conjugate to the free OH exhibit rather low vibrational frequencies (3000-3500 cm(-1)); (ii) the presence of a significant fraction (>10%) of free and randomly oriented water molecules at the interface ("labile water"), neither of whose OH groups are strong H-bond donors; (iii) the inertial rotation of free OH groups, especially from the labile water, contribute to the population decay of excited free OH groups with comparable rate and magnitude as intramolecular energy transfer between the OH groups. These results suggest that the labile water, which might not be easily detectable by the conventional vibrational sum frequency generation method, plays an important role in the surface water dynamics.

  11. Hydrogen bonding and vibrational energy relaxation of interfacial water: A full DFT molecular dynamics simulation

    Science.gov (United States)

    Jeon, Jonggu; Hsieh, Cho-Shuen; Nagata, Yuki; Bonn, Mischa; Cho, Minhaeng

    2017-07-01

    The air-water interface has been a subject of extensive theoretical and experimental studies due to its ubiquity in nature and its importance as a model system for aqueous hydrophobic interfaces. We report on the structure and vibrational energy transfer dynamics of this interfacial water system studied with equilibrium and non-equilibrium molecular dynamics simulations employing a density functional theory -based description of the system and the kinetic energy spectral density analysis. The interfacial water molecules are found to make fewer and weaker hydrogen (H)-bonds on average compared to those in the bulk. We also find that (i) the H-bonded OH groups conjugate to the free OH exhibit rather low vibrational frequencies (3000-3500 cm-1); (ii) the presence of a significant fraction (>10%) of free and randomly oriented water molecules at the interface ("labile water"), neither of whose OH groups are strong H-bond donors; (iii) the inertial rotation of free OH groups, especially from the labile water, contribute to the population decay of excited free OH groups with comparable rate and magnitude as intramolecular energy transfer between the OH groups. These results suggest that the labile water, which might not be easily detectable by the conventional vibrational sum frequency generation method, plays an important role in the surface water dynamics.

  12. Molecular Dynamics Simulations of Aqueous and Confined Systems Relevant to the Supercritical Water Cooled Nuclear Reactor

    Science.gov (United States)

    Kallikragas, Dimitrios Theofanis

    Supercritical water (SCW) is the intended heat transfer fluid and potential neutron moderator in the proposed GEN-IV Supercritical Water Cooled Reactor (SCWR). The oxidative environment poses challenges in choosing appropriate design materials, and the behaviour of SCW within crevices of the passivation layer is needed for developing a corrosion control strategy to minimize corrosion. Molecular Dynamics simulations have been employed to obtain diffusion coefficients, coordination number and surface density characteristics, of water and chloride in nanometer-spaced iron hydroxide surfaces. Diffusion models for hydrazine are evaluated along with hydration data. Results demonstrate that water is more likely to accumulate on the surface at low density conditions. The effect of confinement on the water structure diminishes as the gap size increases. The diffusion coefficient of chloride decreases with larger surface spacing. Clustering of water at the surface implies that the SCWR will be most susceptible to pitting corrosion and stress corrosion cracking.

  13. Water-mediated conformational transitions in nicotinic receptor M2 helix bundles: a molecular dynamics study.

    Science.gov (United States)

    Sankararamakrishnan, R; Sansom, M S

    1995-12-27

    The ion channel of the nicotinic acetylcholine receptor is a water-filled pore formed by five M2 helix segments, one from each subunit. Molecular dynamics simulations on bundles of five M2 alpha 7 helices surrounding a central column of water and with caps of water molecules at either end of the pore have been used to explore the effects of intrapore water on helix packing. Interactions of water molecules with the N-terminal polar sidechains lead to a conformational transition from right- to left-handed supercoils during these stimulations. These studies reveal that the pore formed by the bundle of M2 helices is flexible. A structural role is proposed for water molecules in determining the geometry of bundles of isolated pore-forming helices.

  14. The Effect of Water on the Work of Adhesion at Epoxy Interfaces by Molecular Dynamics Simulation

    Science.gov (United States)

    Hinkley, J.A.; Frankland, S.J.V.; Clancy, T.C.

    2009-01-01

    Molecular dynamics simulation can be used to explore the detailed effects of chemistry on properties of materials. In this paper, two different epoxies found in aerospace resins are modeled using molecular dynamics. The first material, an amine-cured tetrafunctional epoxy, represents a composite matrix resin, while the second represents a 177 C-cured adhesive. Surface energies are derived for both epoxies and the work of adhesion values calculated for the epoxy/epoxy interfaces agree with experiment. Adding water -- to simulate the effect of moisture exposure -- reduced the work of adhesion in one case, and increased it in the other. To explore the difference, the various energy terms that make up the net work of adhesion were compared and the location of the added water was examined.

  15. Molecular Dynamics Analysis of Lysozyme Protein in Ethanol- Water Mixed Solvent

    Science.gov (United States)

    2012-01-01

    Hermans , 1981; Levitt & Warshel, 1975). The idea for molecular dynamic simulation was born out of the quest to solve and understand the following  To...GROMACS is the MD analysis code employed in the present work. Groningen machine for chemical simulations( GROMACS)(Lindahl, Hess , & Van Der Spoel...Physical Chemistry B, 106(14), 3668-3672. Berendsen, H., Postma, J., Van Gunsteren, W., & Hermans , J. (1981). Interaction models for water in

  16. Hydrogen Bonding and Related Properties in Liquid Water: A Car-Parrinello Molecular Dynamics Simulation Study.

    Science.gov (United States)

    Guardia, Elvira; Skarmoutsos, Ioannis; Masia, Marco

    2015-07-23

    The local hydrogen-bonding structure and dynamics of liquid water have been investigated using the Car-Parrinello molecular dynamics simulation technique. The radial distribution functions and coordination numbers around water molecules have been found to be strongly dependent on the number of hydrogen bonds formed by each molecule, revealing also the existence of local structural heterogeneities in the structure of the liquid. The results obtained have also revealed the strong effect of the local hydrogen-bonding network on the local tetrahedral structure and entropy. The investigation of the dynamics of the local hydrogen-bonding network in liquid water has shown that this network is very labile, and the hydrogen bonds break and reform very rapidly. Nevertheless, it has been found that the hydrogen-bonding states associated with the formation of four hydrogen bonds by a water molecule exhibit the largest survival probability and corresponding lifetime. The reorientational motions of water molecules have also been found to be strongly dependent on their initial hydrogen-bonding state. Finally, the dependence of the librational and vibrational modes of water molecules on the local hydrogen-bonding network has been carefully examined, revealing a significant effect upon the libration and bond-stretching peak frequencies. The calculated low frequency peaks come in agreement with previously reported interpretations of the experimental low-frequency Raman spectrum of liquid water.

  17. Nonequilibrium molecular dynamics simulation of water transport through carbon nanotube membranes at low pressurea)

    Science.gov (United States)

    Wang, Luying; Dumont, Randall S.; Dickson, James M.

    2012-07-01

    Nonequilibrium molecular dynamics (NEMD) simulations are used to investigate pressure-driven water flow passing through carbon nanotube (CNT) membranes at low pressures (5.0 MPa) typical of real nanofiltration (NF) systems. The CNT membrane is modeled as a simplified NF membrane with smooth surfaces, and uniform straight pores of typical NF pore sizes. A NEMD simulation system is constructed to study the effects of the membrane structure (pores size and membrane thickness) on the pure water transport properties. All simulations are run under operating conditions (temperature and pressure difference) similar to a real NF processes. Simulation results are analyzed to obtain water flux, density, and velocity distributions along both the flow and radial directions. Results show that water flow through a CNT membrane under a pressure difference has the unique transport properties of very fast flow and a non-parabolic radial distribution of velocities which cannot be represented by the Hagen-Poiseuille or Navier-Stokes equations. Density distributions along radial and flow directions show that water molecules in the CNT form layers with an oscillatory density profile, and have a lower average density than in the bulk flow. The NEMD simulations provide direct access to dynamic aspects of water flow through a CNT membrane and give a view of the pressure-driven transport phenomena on a molecular scale.

  18. Molecular dynamics study of water molecule diffusion in oil-paper insulation materials

    Science.gov (United States)

    Liao, Rui-Jin; Zhu, Meng-Zhao; Yang, Li-Jun; Zhou, Xin; Gong, Chun-Yan

    2011-03-01

    Moisture is an important factor that influences the safe operation of transformers. In this study, molecular dynamics was employed to investigate the diffusion behavior of water molecules in the oil-paper insulation materials of transformers. Two oil-cellulose models were built. In the first model, water molecules were initially distributed in oil, and in the second model, water molecules were distributed in cellulose. The non-bonding energies of interaction between water molecules and oil, and between water molecules and cellulose, were calculated by the Dreiding force field. The interaction energy was found to play a dominant role in influencing the equilibrium distribution of water molecules. The radial direction functions of water molecules toward oil and cellulose indicate that the hydrogen bonds between water molecules and cellulose are sufficiently strong to withstand the operating temperature of the transformer. Mean-square displacement analysis of water molecules diffusion suggests that water molecules initially distributed in oil showed anisotropic diffusion; they tended to diffuse toward cellulose. Water molecules initially distributed in cellulose diffused isotropically. This study provides a theoretical contribution for improvements in online monitoring of water in transformers, and for subsequent research on new insulation materials.

  19. Water self-diffusivity confined in graphene nanogap using molecular dynamics simulations

    Science.gov (United States)

    Moulod, M.; Hwang, G.

    2016-11-01

    Fundamental understanding of water confined in graphene is crucial to optimally design and operate sustainable energy, water desalination, and bio-medical systems. However, the current understanding predominantly remains in the static properties near the graphene surfaces. In this paper, a key water transport property, i.e., self-diffusivity, is examined under confinement by various graphene nanogap sizes (Lz = 0.7-4.17 nm), using molecular dynamics simulations with various graphene-water interatomic potentials (Simple Point Charge (SPC/E) and TIP3P water models). It is found that the water self-diffusivity nearly linearly decreases as the graphene-water interatomic potential energy increases at a given nanogap size. It also decreases as the graphene nanogap size decreases down to Lz = 1.34 nm; however, it shows the peak water self-diffusivity at Lz = 0.8 nm and then continues to decrease. The peak water self-diffusivity is related to the significant change of the overlapping surface force, and associated, nonlinear local water density distribution. The in-plane water self-diffusivity is higher up to nearly an order of magnitude than that of the out-of-plane due to the geometrical confinement effect by the graphene nanogap. The obtained results provide a roadmap to fundamentally understand the water transport properties in the graphene geometries and surface interactions.

  20. Molecular dynamics of dewetting of ultra-thin water films on solid substrate

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    Molecular dynamics simulation is applied to study the instability and rupture process of ultra-thin water films on a solid substrate. Results show the small disturbance of the film will develop linearly due to the spinodal instability, whereas the interaction between solid and liquid has less influences on the initial growth. Then the rupture occurs and the rim recedes with a dynamic contact angle. The radius of the rim varies with time as the square root of t, which is consistent with the macroscopic theory available.Stronger interaction between solid and liquid will postpone rupture time, decline the dynamic contact angle and raise the density of water near the interface between solid and liquid.

  1. Compressive characteristics of single walled carbon nanotube with water interactions investigated by using molecular dynamics simulation

    Science.gov (United States)

    Wong, C. H.; Vijayaraghavan, V.

    2014-01-01

    The elastic properties of single walled carbon nanotube (SWCNT) with surrounding water interactions are studied using molecular dynamics simulation technique. The compressive loading characteristic of carbon nanotubes (CNTs) in a fluidic medium such as water is critical for its role in determining the lifetime and stability of CNT based nano-fluidic devices. In this paper, we conducted a comprehensive analysis on the effect of geometry, chirality and density of encapsulated water on the elastic properties of SWCNT. Our studies show that defect density and distribution can strongly impact the compressive resistance of SWCNTs in water. Further studies were conducted on capped SWCNTs with varying densities of encapsulated water, which is necessary to understand the strength of CNT as a potential drug carrier. The results obtained from this paper will help determining the potential applications of CNTs in the field of nano-electromechanical systems (NEMS) such as nano-biological and nano-fluidic devices.

  2. Compressive characteristics of single walled carbon nanotube with water interactions investigated by using molecular dynamics simulation

    Energy Technology Data Exchange (ETDEWEB)

    Wong, C.H., E-mail: chwong@ntu.edu.sg; Vijayaraghavan, V.

    2014-01-24

    The elastic properties of single walled carbon nanotube (SWCNT) with surrounding water interactions are studied using molecular dynamics simulation technique. The compressive loading characteristic of carbon nanotubes (CNTs) in a fluidic medium such as water is critical for its role in determining the lifetime and stability of CNT based nano-fluidic devices. In this paper, we conducted a comprehensive analysis on the effect of geometry, chirality and density of encapsulated water on the elastic properties of SWCNT. Our studies show that defect density and distribution can strongly impact the compressive resistance of SWCNTs in water. Further studies were conducted on capped SWCNTs with varying densities of encapsulated water, which is necessary to understand the strength of CNT as a potential drug carrier. The results obtained from this paper will help determining the potential applications of CNTs in the field of nano-electromechanical systems (NEMS) such as nano-biological and nano-fluidic devices.

  3. Wetting and evaporation of salt-water nanodroplets: A molecular dynamics investigation

    OpenAIRE

    Zhang, Jun; Borg, Matthew; Sefiane, Khellil; Reese, Jason

    2015-01-01

    We employ molecular dynamics simulations to study the wetting and evaporation of salt-water nanodroplets on platinum surfaces. Our results show that the contact angle of the droplets increases with the salt concentration. To verify this, a second simulation system of a thin salt-water film on a platinum surface is used to calculate the various surface tensions. We find that both the solid-liquid and liquid-vapor surface tensions increase with salt concentration and as a result these cause an ...

  4. Static and dynamic length scales in supercooled liquids: insights from molecular dynamics simulations of water and tri-propylene oxide.

    Science.gov (United States)

    Klameth, F; Henritzi, P; Vogel, M

    2014-04-14

    We perform molecular dynamics simulations to study static and dynamic length scales in molecular supercooled liquids, in particular, water. For a determination of these scales, we use equilibrium configurations and pin appropriate subsets of molecules so as to obtain random matrices, cylindrical pores, and slit confinements. Static length scales ξ(s) are determined by analyzing overlap correlation functions for various fractions of pinned molecules or distances to the confining walls. For water in all confinements and for propylene oxide trimers in random geometry, a linear increase of ξ(s) with inverse temperature is found. Dynamic length scales ξ(d) are determined by analogous analysis of fraction-dependent or position-resolved correlation times of structural relaxation. While ξ(d) continuously grows upon cooling in the cylindrical and slit confinements, we find no evidence for a temperature dependence in random matrices, implying that molecular dynamics in parsed volumes is qualitatively different from that in bulk liquids. Finally, we study possible connections between the growth of the static and dynamic length scales and the slowdown of the structural relaxation of the supercooled bulk liquids. For water, we observe a linear relation between ln τ(α) and ξ(s)²/T in the whole accessible range down to the critical temperature of mode-coupling theory, T(c). In the weakly supercooled regime, the same relation holds also for ξ(d), as obtained from cylindrical and slit confinements, but deviations from this behavior are observed near T(c). The results are discussed in connection with random first-order theory and experimental studies of liquid dynamics in nanoscopic confinements and binary mixtures.

  5. Molecular dynamics simulation of single-walled silicon carbide nanotubes immersed in water.

    Science.gov (United States)

    Taghavi, Fariba; Javadian, Soheila; Hashemianzadeh, Seyed Majid

    2013-07-01

    The structure and dynamics of water confined in single-walled silicon carbon nanotubes (SWSiCNTs) are investigated using molecular dynamics (MD) simulations. The density of water inside SWSiCNTs is reported, and an equation is suggested to predict the density of water inside SWSiCNTs. Interestingly, the water diffusion coefficients (D) here are larger compared with those in SWCNTs and single-walled boron-nitride nanotubes (SWBNNTs). Furthermore, water inside zigzag SWCNTs has a lower diffusion coefficient than water inside armchair SWCNTs. A thorough analysis of the density profiles, hydrogen bonding, and water molecule orientation inside SWSiCNTs is presented to explore the mechanism behind the diffusive behavior of water observed here. It is shown here, by mean square displacement (MSD) analysis, that water molecules inside SWSiCNTs diffuse with a ballistic motion mechanism for up to 500ps. Additionally it is confirmed here for the first time that water molecules confined in the SWSiCNTs with diameters of less than 10Å obey the single-file diffusion mechanism at time scales in excess of 500ps. The orientation of water molecules inside SWSiCNTs could be a good explanation for the difference between the diffusion coefficient in (6,6) and (10,0) SWSiCNTs. Finally, a PMF analysis explains the difficulty of water entrance into SWSiCNTs and also the different water self-diffusion inside armchair and zigzag SWSiCNTs. These results are motivating reasons to use SWSiCNTs in nanoscale biochannels, for instance, in drug-delivery applications.

  6. Molecular Dynamics Simulations of a Cyclic DP-240 Amylose Fragment in a Periodic Cell: Glass Transition Temperature and Water Diffusion

    Science.gov (United States)

    Molecular dynamics simulations using AMB06C, an in-house carbohydrate force field, (NPT ensembles, 1atm) were carried out on a periodic cell that contained a cyclic-DP-240 amylose fragment and TIP3P water molecules. Molecular conformation and movement of the amylose fragment and water molecules at ...

  7. Hydrogen Bonding and Dielectric Spectra of Ethylene Glycol–Water Mixtures from Molecular Dynamics Simulations

    Science.gov (United States)

    2016-01-01

    Mixtures of ethylene glycol with water are a prominent example of media with variable viscosity. Classical molecular dynamics simulations at room temperature were performed for mixtures of ethylene glycol (EG) and water with EG mole fractions of xE = 0.0, 0.1, 0.2, 0.4, 0.6, 0.9, 1.0. The calculated dielectric loss spectra were in qualitative agreement with experiment. We found a slightly overestimated slowdown of the dynamics with increasing EG concentration compared to experimental data. Statistics of the hydrogen bond network and hydrogen bond lifetimes were derived from suitable time correlation functions and also show a slowdown in the dynamics with increasing xE. A similar picture is predicted for the time scales of EG conformer changes and for molecular reorientation. A slight blue shift was obtained for the power spectra of the molecular center of mass motion. The results were used to give a qualitative interpretation of the origin of three different relaxation times that appear in experimental complex dielectric spectra and of their change with xE. PMID:27649083

  8. Isomerization reaction dynamics and equilibrium at the liquid-vapor interface of water. A molecular-dynamics study

    Science.gov (United States)

    Benjamin, Ilan; Pohorille, Andrew

    1993-01-01

    The gauche-trans isomerization reaction of 1,2-dichloroethane at the liquid-vapor interface of water is studied using molecular-dynamics computer simulations. The solvent bulk and surface effects on the torsional potential of mean force and on barrier recrossing dynamics are computed. The isomerization reaction involves a large change in the electric dipole moment, and as a result the trans/gauche ratio is considerably affected by the transition from the bulk solvent to the surface. Reactive flux correlation function calculations of the reaction rate reveal that deviation from the transition-state theory due to barrier recrossing is greater at the surface than in the bulk water. This suggests that the system exhibits non-Rice-Ramsperger-Kassel-Marcus behavior due to the weak solvent-solute coupling at the water liquid-vapor interface.

  9. Isomerization reaction dynamics and equilibrium at the liquid-vapor interface of water. A molecular-dynamics study

    Science.gov (United States)

    Benjamin, Ilan; Pohorille, Andrew

    1993-01-01

    The gauche-trans isomerization reaction of 1,2-dichloroethane at the liquid-vapor interface of water is studied using molecular-dynamics computer simulations. The solvent bulk and surface effects on the torsional potential of mean force and on barrier recrossing dynamics are computed. The isomerization reaction involves a large change in the electric dipole moment, and as a result the trans/gauche ratio is considerably affected by the transition from the bulk solvent to the surface. Reactive flux correlation function calculations of the reaction rate reveal that deviation from the transition-state theory due to barrier recrossing is greater at the surface than in the bulk water. This suggests that the system exhibits non-Rice-Ramsperger-Kassel-Marcus behavior due to the weak solvent-solute coupling at the water liquid-vapor interface.

  10. Calculation of heat capacities of light and heavy water by path-integral molecular dynamics

    Science.gov (United States)

    Shiga, Motoyuki; Shinoda, Wataru

    2005-10-01

    As an application of atomistic simulation methods to heat capacities, path-integral molecular dynamics has been used to calculate the constant-volume heat capacities of light and heavy water in the gas, liquid, and solid phases. While the classical simulation based on conventional molecular dynamics has estimated the heat capacities too high, the quantum simulation based on path-integral molecular dynamics has given reasonable results based on the simple point-charge/flexible potential model. The calculated heat capacities (divided by the Boltzmann constant) in the quantum simulation are 3.1 in the vapor H2O at 300 K, 6.9 in the liquid H2O at 300 K, and 4.1 in the ice IhH2O at 250 K, respectively, which are comparable to the experimental data of 3.04, 8.9, and 4.1, respectively. The quantum simulation also reproduces the isotope effect. The heat capacity in the liquid D2O has been calculated to be 10% higher than that of H2O, while it is 13% higher in the experiment. The results demonstrate that the path-integral simulation is a promising approach to quantitatively evaluate the heat capacities for molecular systems, taking account of quantum-mechanical vibrations as well as strongly anharmonic motions.

  11. Comparison of path integral molecular dynamics methods for the infrared absorption spectrum of liquid water

    Science.gov (United States)

    Habershon, Scott; Fanourgakis, George S.; Manolopoulos, David E.

    2008-08-01

    The ring polymer molecular dynamics (RPMD) and partially adiabatic centroid molecular dynamics (PA-CMD) methods are compared and contrasted in an application to the infrared absorption spectrum of a recently parametrized flexible, polarizable, Thole-type potential energy model for liquid water. Both methods predict very similar spectra in the low-frequency librational and intramolecular bending region at wavenumbers below 2500 cm-1. However, the RPMD spectrum is contaminated in the high-frequency O-H stretching region by contributions from the internal vibrational modes of the ring polymer. This problem is avoided in the PA-CMD method, which adjusts the elements of the Parrinello-Rahman mass matrix so as to shift the frequencies of these vibrational modes beyond the spectral range of interest. PA-CMD does not require any more computational effort than RPMD and it is clearly the better of the two methods for simulating vibrational spectra.

  12. Molecular Structure and Dynamics of Water on Pristine and Strained Phosphorene: Wetting and Diffusion at Nanoscale

    Science.gov (United States)

    Zhang, Wei; Ye, Chao; Hong, Linbi; Yang, Zaixing; Zhou, Ruhong

    2016-12-01

    Phosphorene, a newly fabricated two-dimensional (2D) nanomaterial, has emerged as a promising material for biomedical applications with great potential. Nonetheless, understanding the wetting and diffusive properties of bio-fluids on phosphorene which are of fundamental importance to these applications remains elusive. In this work, using molecular dynamics (MD) simulations, we investigated the structural and dynamic properties of water on both pristine and strained phosphorene. Our simulations indicate that the diffusion of water molecules on the phosphorene surface is anisotropic, with strain-enhanced diffusion clearly present, which arises from strain-induced smoothing of the energy landscape. The contact angle of water droplet on phosphorene exhibits a non-monotonic variation with the transverse strain. The structure of water on transverse stretched phosphorene is demonstrated to be different from that on longitudinal stretched phosphorene. Moreover, the contact angle of water on strained phosphorene is proportional to the quotient of the longitudinal and transverse diffusion coefficients of the interfacial water. These findings thereby offer helpful insights into the mechanism of the wetting and transport of water at nanoscale, and provide a better foundation for future biomedical applications of phosphorene.

  13. Spontaneous assembly of HSP90 inhibitors at water/octanol interface: A molecular dynamics simulation study

    Science.gov (United States)

    Zolghadr, Amin Reza; Boroomand, Samaneh

    2017-02-01

    Drug absorption at an acceptable dose depends on the pair of solubility and permeability. There are many potent therapeutics that are not active in vivo, presumably due to the lack of capability to cross the cell membrane. Molecular dynamics simulation of radicicol, diol-radicicol, cyclopropane-radicicol and 17-DMAG were performed at water/octanol interface to suggest interfacial activity as a physico-chemical characteristic of these heat shock protein 90 (HSP90) inhibitors. We have observed that orally active HSP90 inhibitors form aggregates at the water/octanol and DPPC-lipid/water interfaces by starting from an initial configuration with HSP90 inhibitors embedded in the water matrix.

  14. Geometric isotope effects on small chloride ion water clusters with path integral molecular dynamics simulations

    Science.gov (United States)

    Wang, Qi; Suzuki, Kimichi; Nagashima, Umpei; Tachikawa, Masanori; Yan, Shiwei

    2013-11-01

    The geometric isotope effects on the structures of hydrated chloride ionic hydrogen bonded clusters are explored by carrying out path integral molecular dynamics simulations. First, an outer shell coordinate is selected to display the rearrangement of single and multi hydration shell cluster structures. Next, to show the competition of intramolecular and intermolecular nuclear quantum effects, the intramolecular OH∗ stretching and intermolecular ion-water wagging motions are studied for single and multi shell structures, respectively. The results indicate that the intermolecular nuclear quantum effects stabilize the ionic hydrogen bonds in single shell structures, while they are destabilized through the competition with intramolecular nuclear quantum effects in multi shell structures. In addition, the correlations between ion-water stretching motion and other cluster vibrational coordinates are discussed. The results indicate that the intermolecular nuclear quantum effects on the cluster structures are strongly related to the cooperation of the water-water hydrogen bond interactions.

  15. Molecular dynamics simulations of water on a hydrophilic silica surface at high air pressures

    DEFF Research Database (Denmark)

    Zambrano, H.A.; Walther, Jens Honore; Jaffe, R.L.

    2014-01-01

    of air in water at different pressures. Using the calibrated force field, we conduct MD simulations to study the interface between a hydrophilic silica substrate and water surrounded by air at different pressures. We find that the static water contact angle is independent of the air pressure imposed......Wepresent a force field forMolecular Dynamics (MD) simulations ofwater and air in contactwith an amorphous silica surface. We calibrate the interactions of each species present in the systemusing dedicated criteria such as the contact angle of a water droplet on a silica surface, and the solubility...... on the system. Our simulations reveal the presence of a nanometer thick layer of gas at the water–silica interface. We believe that this gas layer could promote nucleation and stabilization of surface nanobubbles at amorphous silica surfaces. © 2014 Elsevier B.V. All rights reserved....

  16. Molecular Dynamics Simulation of Water Nanodroplets on Silica Surfaces at High Air Pressures

    DEFF Research Database (Denmark)

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

    2010-01-01

    e.g., nanobubbles. In the present work we study the role of air on the wetting of hydrophilic systems. We conduct molecular dynamics simulations of a water nanodroplet on an amorphous silica surface at different air pressures. The interaction potentials describing the silica, water, and air...... not been reached. Contact angle measurements of droplets on solid surfaces offer useful quantitative measurements of the physiochemical properties of the solid-liquid interface. For hydrophobic systems the properties the solid- liquid interface are now known to be strongly influenced by the presence of air...... are obtained from the literature. The silica surface is modeled by a large 32 ⨯ 32 ⨯ 2 nm amorphous SiO2 structure consisting of 180000 atoms. The water consists of 18000 water molecules surrounded by N2 and O2 air molecules corresponding to air pressures of 0 bar (vacuum), 50 bar, 100 bar and 200 bar. We...

  17. Optimizing Water Transport through Graphene-Based Membranes: Insights from Nonequilibrium Molecular Dynamics.

    Science.gov (United States)

    Muscatello, Jordan; Jaeger, Frederike; Matar, Omar K; Müller, Erich A

    2016-05-18

    Recent experimental results suggest that stacked layers of graphene oxide exhibit strong selective permeability to water. To construe this observation, the transport mechanism of water permeating through a membrane consisting of layered graphene sheets is investigated via nonequilibrium and equilibrium molecular dynamics simulations. The effect of sheet geometry is studied by changing the offset between the entrance and exit slits of the membrane. The simulation results reveal that the permeability is not solely dominated by entrance effects; the path traversed by water molecules has a considerable impact on the permeability. We show that contrary to speculation in the literature, water molecules do not pass through the membrane as a hydrogen-bonded chain; instead, they form well-mixed fluid regions confined between the graphene sheets. The results of the present work are used to provide guidelines for the development of graphene and graphene oxide membranes for desalination and solvent separation.

  18. Molecular dynamics simulations of the surface tension of oxygen-supersaturated water

    Directory of Open Access Journals (Sweden)

    S. Jain

    2017-04-01

    Full Text Available In this work, non-reactive molecular dynamic simulations were conducted to determine the surface tension of water as a function of the concentration of the dissolved gaseous molecules (O2, which would in turn help to predict the pressure inside the nanobubbles under supersaturation conditions. Knowing the bubble pressure is a prerequisite for understanding the mechanisms behind the spontaneous combustion of the H2/O2 gases inside the nanobubbles. First, the surface tension of pure water was determined using the planar interface method and the Irving and Kirkwood formula. Next, the surface tension of water containing four different supersaturation concentrations (S of O2 gas molecules was computed considering the curved interface of a nanobubble. The surface tension of water was found to decrease with an increase in the supersaturation ratio or the concentration of the dissolved O2 gas molecules.

  19. Molecular dynamics simulation of nanoscale distribution and mobility of water and dimethylmethylphosphonate in sulfonated polystyrene.

    Science.gov (United States)

    Vishnyakov, Aleksey; Neimark, Alexander V

    2008-11-27

    The interest in a better understanding of the specific interactions of phosphor-organic compounds and water with sulfonated polystyrene (sPS) is motivated by the use of block copolymers as protective membranes against chemical warfare agents. Using classical molecular dynamics simulations, we explored the nanoscale segregation and diffusion of water and nerve gas simulant dimethylmethylphosphonate (DMMP) in sPS neutralized with calcium counterions at different sulfonation and hydration levels. The water content was varied from 15 to 54% of dry polymer weight, and the DMMP content was varied from 0 to 100 wt %. We found that, in the 40% sulfonated polystyrene, water forms well defined aggregates, which grow in size as the hydration increases, reaching approximately 20 A at the maximum water content. In the 100% sulfonated polystyrene, the overall structure of hydrated polymer is more uniform with smaller water aggregates. Diffusion of water at the same number of water molecules per sulfonate group is faster at a lower sulfonation level. The solvation of sPS in water-DMMP binary mixtures was found to differ substantially from Nafion, where DMMP forms a layer between the hydropholic and hydrophobic subphases. In sPS with divalent Ca(2+) counterions, DMMP and water compete for the solvation of the sulfonate group. At high water and DMMP contents, the diffusion of DMMP turned out to be rather fast with a diffusion coefficient of ca. 30% of that of water. At the same time, water diffusion slows down as the DMMP concentration increases. This observation suggests that although sPS is permeable for both solvents, water and DMMP are partially segregated on the scale of 1-2 nm and have different pathways through the system. The nonuniform nanoscale distribution of water and DMMP in sPS is confirmed by analyses of different pair correlation functions. This feature may significantly affect the perm-selective properties of sPS-contained block copolymer membranes.

  20. Molecular dynamics simulations of the orthoclase (001)- and (010)-water interfaces

    Energy Technology Data Exchange (ETDEWEB)

    Kerisit, Sebastien N.; Liu, Chongxuan; Ilton, Eugene S.

    2008-03-15

    Molecular dynamics simulations of water in contact with the (001) and (010) surfaces of orthoclase (KAlSi3O8) were carried out to investigate the structure and dynamics of the feldspar-water interface, contrast the intrinsic structural properties of the two surfaces, and provide a basis for future work on the diffusion of ions and molecules in microscopic mineral fractures. Electron density profiles were computed from the molecular dynamics trajectories and compared with those derived experimentally from high-resolution X-ray reflectivity measurements by Fenter and co-workers (Fenter et al., 2003a). For each surface, three scenarios were considered whereby the interfacial species is potassium, water, or a hydronium ion. Excellent agreement was obtained for the (001) surface when potassium is the predominant interfacial species. Good agreement was found for the (010) surface with some discrepancies which could be due in part to the fact that our model does not take into account the increased roughness of the (010) surface compared to the (001) surface. The two surfaces showed similarities in the extent of water ordering at the interface, the activation energies for water and potassium desorption, and the adsorption localization of interfacial species. However, there are also important differences between the two surfaces in the coordination of a given adsorbed species, adsorption sites density, and the propensity for water molecules in the adsorbed and first hydration layers to coordinate to surface bridging oxygen atoms. These differences may have implications for the extent of dissolution in the proton-promoted regime since hydrolysis of Si(Al)-O-Si(Al) bonds is thought to be the major dissolution mechanism.

  1. Semiquantal molecular dynamics simulations of hydrogen-bond dynamics in liquid water using multi-dimensional Gaussian wave packets.

    Science.gov (United States)

    Ono, Junichi; Ando, Koji

    2012-11-01

    A semiquantal (SQ) molecular dynamics (MD) simulation method based on an extended Hamiltonian formulation has been developed using multi-dimensional thawed gaussian wave packets (WPs), and applied to an analysis of hydrogen-bond (H-bond) dynamics in liquid water. A set of Hamilton's equations of motion in an extended phase space, which includes variance-covariance matrix elements as auxiliary coordinates representing anisotropic delocalization of the WPs, is derived from the time-dependent variational principle. The present theory allows us to perform real-time and real-space SQMD simulations and analyze nuclear quantum effects on dynamics in large molecular systems in terms of anisotropic fluctuations of the WPs. Introducing the Liouville operator formalism in the extended phase space, we have also developed an explicit symplectic algorithm for the numerical integration, which can provide greater stability in the long-time SQMD simulations. The application of the present theory to H-bond dynamics in liquid water is carried out under a single-particle approximation in which the variance-covariance matrix and the corresponding canonically conjugate matrix are reduced to block-diagonal structures by neglecting the interparticle correlations. As a result, it is found that the anisotropy of the WPs is indispensable for reproducing the disordered H-bond network compared to the classical counterpart with the use of the potential model providing competing quantum effects between intra- and intermolecular zero-point fluctuations. In addition, the significant WP delocalization along the out-of-plane direction of the jumping hydrogen atom associated with the concerted breaking and forming of H-bonds has been detected in the H-bond exchange mechanism. The relevance of the dynamical WP broadening to the relaxation of H-bond number fluctuations has also been discussed. The present SQ method provides the novel framework for investigating nuclear quantum dynamics in the many

  2. Nano-confined water in the interlayers of hydrocalumite: Reorientational dynamics probed by neutron spectroscopy and molecular dynamics computer simulations

    Science.gov (United States)

    Kalinichev, A. G.; Faraone, A.; Udovic, T.; Kolesnikov, A. I.; de Souza, N. R.; Reinholdt, M. X.; Kirkpatrick, R.

    2008-12-01

    Layered double hydroxides (LDHs, anionic clays) represent excellent model systems for detailed molecular- level studies of the structure, dynamics, and energetics of nano-confined water in mineral interlayers and nano-pores, because LDH interlayers can have a well-defined structures and contain H2O molecules and a wide variety of anions in structurally well-defined positions and coordinations. [Ca2Al(OH)6]Cl·2H2O, also known as hydrocalumite or Friedel's salt, has a well- ordered Ca,Al distribution in the hydroxide layer and a very high degree of H2O,Cl ordering in the interlayer. It is also one of the only LDH phase for which a single crystal structure refinement is available. Thus, it is currently the best model compound for understanding the structure and dynamical behavior of interlayer and surface species in other, less-ordered, LDHs. We investigated the structural and dynamic behavior of water in the interlayers of hydrocalumite using inelastic (INS) and quasielastic (QENS) neutron scattering and molecular dynamics computer simulations. The comperehensive neutron scattering studies were performed for one fully hydrated and one dehydrated sample of hydrocalumite using several complementary instruments (HFBS, DCS and FANS at NCNR; HRMECS and QENS at IPNS) at temperatures above and below the previously discovered order-disorder interlayer phase transition. Together the experimental and molecular modeling results capture the important details of the dynamics of nano-confined water and the effects of the orientational ordering of H2O molecules above and below the phase transition. They provide otherwise unobtainable experimental information about the transformation of H2O librational and diffusional modes across the order-disorder phase transition and significantly add to our current understanding of the structure and dynamics of water in LDH phases based on the earlier NMR, IR, X-ray, and calorimetric measurements. The approach can now be extended to probe the

  3. Molecular dynamics simulation of the structure and dynamics of water-1-alkyl-3-methylimidazolium ionic liquid mixtures.

    Science.gov (United States)

    Méndez-Morales, Trinidad; Carrete, Jesús; Cabeza, Oscar; Gallego, Luis J; Varela, Luis M

    2011-06-02

    We have performed extensive molecular dynamic simulations to analyze the influence of cation and anion natures, and of water concentration, on the structure and dynamics of water-1-alkyl-3-methylimidazolium ionic liquid mixtures. The dependence on water concentration of the radial distribution functions, coordination numbers, and hydrogen bonding degree between the different species has been systematically analyzed for different lengths of the cation alkyl chain (alkyl = ethyl, butyl, hexyl, and octyl) and several counterions. These include two halogens of different sizes and positions in Hoffmeister series, Cl(-) and Br(-), and the highly hydrophobic inorganic anion PF(6)(-) throughout its whole solubility regime. The formation of water clusters in the mixture has been verified, and the influences of both anion hydrophobicity and cation chain length on the structure and size of these clusters have been analyzed. The water cluster size is shown to be relatively independent of the cation chain length, but strongly dependent on the hydrophobicity of the anion, which also determines critically the network formation of water and therefore the miscibility of the ionic liquid. The greater influence of the anion relative to the cation one is seen to be reflected in all the analyzed physical properties. Finally, single-particle dynamics in IL-water mixtures is considered, obtaining the self-diffusion coefficients and the velocity autocorrelation functions of water molecules in the mixture, and analyzing the effect of cation, anion, and water concentration on the duration of the ballistic regime and on the time of transition to the diffusive regime. Complex non-Markovian behavior was detected at intermediate times within an interval progressively shorter as water concentration increases.

  4. Solubility of cellulose in supercritical water studied by molecular dynamics simulations.

    Science.gov (United States)

    Tolonen, Lasse K; Bergenstråhle-Wohlert, Malin; Sixta, Herbert; Wohlert, Jakob

    2015-04-02

    The insolubility of cellulose in ambient water and most aqueous systems presents a major scientific and practical challenge. Intriguingly though, the dissolution of cellulose has been reported to occur in supercritical water. In this study, cellulose solubility in ambient and supercritical water of varying density (0.2, 0.7, and 1.0 g cm(-3)) was studied by atomistic molecular dynamics simulations using the CHARMM36 force field and TIP3P water. The Gibbs energy of dissolution was determined between a nanocrystal (4 × 4 × 20 anhydroglucose residues) and a fully dissociated state using the two-phase thermodynamics model. The analysis of Gibbs energy suggested that cellulose is soluble in supercritical water at each of the studied densities and that cellulose dissolution is typically driven by the entropy gain upon the chain dissociation while simultaneously hindered by the loss of solvent entropy. Chain dissociation caused density augmentation around the cellulose chains, which improved water-water bonding in low density supercritical water whereas the opposite occurred in ambient and high density supercritical water.

  5. Molecular Dynamics Simulation of Diffusion of Vitamin C in Water Solution%Molecular Dynamics Simulation of Diffusion of Vitamin C in Water Solution

    Institute of Scientific and Technical Information of China (English)

    曾建平; 王爱民; 贡雪东; 陈景文; 陈松; 薛锋

    2012-01-01

    Under different temperatures and concentrations, the diffusion of Vitamin C (VC) in water solution was exam- ined by molecular dynamics simulation. The diffusion coefficients were calculated based on the Einstein equation. The influences of temperature, concentration, and simulation time on the diffusion coefficient were discussed. The results showed that at higher temperature and lower concentration the normal diffusions appear relatively late, but the linear range of mean square displacement curves continues longer than that at lower temperature and higher concentration. At the same temperature, the normal diffusion time increases and the diffusion coefficient decreases as the simulation concentration increases. These simulation results are in good agreement with experiments. Analyses of the pair correlation functions of the simulation systems showed that hydrogen bonds are mainly formed be- tween the hydrogen atoms of VC molecules and oxygen atoms of H20 molecules, rather than between the O atoms of VC molecules and H atoms of H20 molecules. The diffusion coefficient is higher as the interaction between water molecules and VC molecules is stronger when VC concentration is lower. The water in the model systems affects the diffusion of VC molecules by the short-range repulsion of O(H20)-O(H20) pairs and the non-bond interaction of H(H20)-H(H20) pairs. The short-range repulsion of O(H20)-O(H20) pairs is greater when VC concentration is higher, the diffusion of VC is weaker. The greater the non-bond interaction of H(H20)-H(H20) pairs is, the higher the VC diffusion is. It is expected that this study can provide a theoretical direction for the experiments on the mass transfer of VC in water solution.

  6. Stability and comparative analysis of AOT/water/isooctane reverse micelle system using dynamic light scattering and molecular dynamics.

    Science.gov (United States)

    Vasquez, V R; Williams, B C; Graeve, O A

    2011-03-31

    We use molecular dynamics (MD) and dynamic light scattering (DLS) measurements to analyze the size of reverse micellar structures in the AOT-water-isooctane system at different water-to-surfactant ratios at ambient temperature and pressure. We find good qualitative agreement for the size and morphology behavior of the reverse micelle structures between molecular dynamics calculations and DLS measurements; however, the average values for the reverse micelle size distributions are systematically larger for the DLS measurements. The latter tends to capture the average hydrodynamic size of the structures based on self-diffusion rather than the average physical size as measured in MD simulations, explaining the systematic deviations observed. The combination of MD with DLS allows a better interpretation of the experimental results, in particular for conditions where the structures are nonspherical, commonly observed at lower water-to-surfactant ratios. We also present and analyze the effect of zirconyl chloride on the micellar size distributions in this system. These type of salts are common for reverse micellar synthesis processes. We find that zirconyl chloride affects significantly the size distributions.

  7. A molecular dynamics study of water nucleation using the TIP4P/2005 model

    Science.gov (United States)

    Pérez, Alejandro; Rubio, Angel

    2011-12-01

    Extensive molecular dynamics simulations were conducted using the TIP4P/2005 water model of Abascal and Vega [J. Chem. Phys. 123, 234505 (2005)] to investigate its condensation from supersaturated vapor to liquid at 330 K. The mean first passage time method [J. Wedekind, R. Strey, and D. Reguera, J. Chem. Phys. 126, 134103 (2007); L. S. Bartell and D. T. Wu, 125, 194503 (2006)] was used to analyze the influence of finite size effects, thermostats, and charged species on the nucleation dynamics. We find that the Nosé-Hoover thermostat and the one proposed by Bussi et al. [J. Chem. Phys. 126, 014101 (2007)] give essentially the same averages. We identify the maximum thermostat coupling time to guarantee proper thermostating for these simulations. The presence of charged species has a dramatic impact on the dynamics, inducing a marked change towards a pure growth regime, which highlights the importance of ions in the formation of liquid droplets in the atmosphere. It was found a small but noticeable sign preference at intermediate cluster sizes (between 5 and 30 water molecules) corresponding mostly to the formation of the second solvation shell around the ion. The TIP4P/2005 water model predicts that anions induce faster formation of water clusters than cations of the same magnitude of charge.

  8. Nonequilibrium molecular dynamics simulation of pressure-driven water transport through modified CNT membranes

    Science.gov (United States)

    Wang, Luying; Dumont, Randall S.; Dickson, James M.

    2013-03-01

    Nonequilibrium molecular dynamics (NEMD) simulations are presented to investigate the effect of water-membrane interactions on the transport properties of pressure-driven water flow passing through carbon nanotube (CNT) membranes. The CNT membrane is modified with different physical properties to alter the van der Waals interactions or the electrostatic interactions between water molecules and the CNT membranes. The unmodified and modified CNT membranes are models of simplified nanofiltration (NF) membranes at operating conditions consistent with real NF systems. All NEMD simulations are run with constant pressure difference (8.0 MPa) temperature (300 K), constant pore size (0.643 nm radius for CNT (12, 12)), and membrane thickness (6.0 nm). The water flow rate, density, and velocity (in flow direction) distributions are obtained by analyzing the NEMD simulation results to compare transport through the modified and unmodified CNT membranes. The pressure-driven water flow through CNT membranes is from 11 to 21 times faster than predicted by the Navier-Stokes equations. For water passing through the modified membrane with stronger van der Waals or electrostatic interactions, the fast flow is reduced giving lower flow rates and velocities. These investigations show the effect of water-CNT membrane interactions on water transport under NF operating conditions. This work can help provide and improve the understanding of how these membrane characteristics affect membrane performance for real NF processes.

  9. Molecular Dynamics Simulations Reveal that Water Diffusion between Graphene Oxide Layers is Slow

    Science.gov (United States)

    Devanathan, Ram; Chase-Woods, Dylan; Shin, Yongsoon; Gotthold, David W.

    2016-07-01

    Membranes made of stacked layers of graphene oxide (GO) hold the tantalizing promise of revolutionizing desalination and water filtration if selective transport of molecules can be controlled. We present the findings of an integrated study that combines experiment and molecular dynamics simulation of water intercalated between GO layers. We simulated a range of hydration levels from 1 wt.% to 23.3 wt.% water. The interlayer spacing increased upon hydration from 0.8 nm to 1.1 nm. We also synthesized GO membranes that showed an increase in layer spacing from about 0.7 nm to 0.8 nm and an increase in mass of about 15% on hydration. Water diffusion through GO layers is an order of magnitude slower than that in bulk water, because of strong hydrogen bonded interactions. Most of the water molecules are bound to OH groups even at the highest hydration level. We observed large water clusters that could span graphitic regions, oxidized regions and holes that have been experimentally observed in GO. Slow interlayer diffusion can be consistent with experimentally observed water transport in GO if holes lead to a shorter path length than previously assumed and sorption serves as a key rate-limiting step.

  10. Nonequilibrium molecular dynamics simulation of pressure-driven water transport through modified CNT membranes.

    Science.gov (United States)

    Wang, Luying; Dumont, Randall S; Dickson, James M

    2013-03-28

    Nonequilibrium molecular dynamics (NEMD) simulations are presented to investigate the effect of water-membrane interactions on the transport properties of pressure-driven water flow passing through carbon nanotube (CNT) membranes. The CNT membrane is modified with different physical properties to alter the van der Waals interactions or the electrostatic interactions between water molecules and the CNT membranes. The unmodified and modified CNT membranes are models of simplified nanofiltration (NF) membranes at operating conditions consistent with real NF systems. All NEMD simulations are run with constant pressure difference (8.0 MPa) temperature (300 K), constant pore size (0.643 nm radius for CNT (12, 12)), and membrane thickness (6.0 nm). The water flow rate, density, and velocity (in flow direction) distributions are obtained by analyzing the NEMD simulation results to compare transport through the modified and unmodified CNT membranes. The pressure-driven water flow through CNT membranes is from 11 to 21 times faster than predicted by the Navier-Stokes equations. For water passing through the modified membrane with stronger van der Waals or electrostatic interactions, the fast flow is reduced giving lower flow rates and velocities. These investigations show the effect of water-CNT membrane interactions on water transport under NF operating conditions. This work can help provide and improve the understanding of how these membrane characteristics affect membrane performance for real NF processes.

  11. Enhanced heating of salty ice and water under microwaves: molecular dynamics study.

    Science.gov (United States)

    Tanaka, Motohiko; Sato, Motoyasu

    2008-01-01

    Through the use of molecular dynamics simulations, we have studied the enhanced heating of salty ice and water by the electric field of applied microwaves at 2.5 GHz, and in the range of 2.5-10 GHz for the frequency dependence. We show that water molecules in salty ice are allowed to rotate in response to the microwave electric field to the extent comparable to those in pure water because the molecules in salty ice are loosely tied by hydrogen bonds with adjacent molecules unlike rigidly bonded pure ice. The weakening of hydrogen-bonded network of molecules in salty ice is mainly due to the electrostatic effect of salt ions rather than the short-range geometrical (size) effect of salt since the presence of salt ions with small radii causes similar enhanced heating.

  12. What first principles molecular dynamics can tell us about EXAFS spectroscopy of radioactive heavy metal cations in water

    Energy Technology Data Exchange (ETDEWEB)

    Duvail, M.; Gaigeot, M.P.; Spezia, R. [Lab. Analyse et Modelisation pour la Biologie et l' Environnement, UMR 8587 CNRS, Univ. d' Evry Val d' Essonne, Evry (France); D' Angelo, P. [Dipt. di Chimica, Univ. di Roma La Sapienza (Italy); Vitorge, P. [Lab. Analyse et Modelisation pour la Biologie et l' Environnement, UMR 8587 CNRS, Univ. d' Evry Val d' Essonne, Evry (France); Lab. de Speciation des Radionucleides et Molecules, CEA Saclay, DEN/DPC/SECR, Gif-sur-Yvette (France)

    2009-07-01

    In this paper we show how molecular dynamics simulation can improve comprehension of structure and dynamics of water solvent around heavy cations. In particular, metal-water radial distribution function obtained from molecular dynamics can be used into EXAFS equation to improve the experimental signal fitting. Here we show results on structure and dynamics of Co{sup 2+}, that is a radiocontaminant cation in its isotopic form {sup 60}Co, and lanthanoids(III) that are the chemical analogues of actinides(III) in aqueous solution. (orig.)

  13. Molecular dynamics study of ion capture from water by a model ionophore, tetraprotonated cryptand SC24

    Science.gov (United States)

    Owenson, Brian; Macelroy, Robert D.; Pohorille, Andrew

    1988-01-01

    The molecular dynamics of chloride capture from water by the tetraprotonated cryptand SC24 has been studied for the cases of 19 distances between the criptand and the chloride. The chloride capture is found to be characterized by a rapid cooperative change in the conformation of the cryptand when the Cl(-) begins to enter the ligand and just as it encounters the energy barrier. The conformational transition is associated with a shift of three N-H bonds from the pure endo orientation, such that they point toward the chloride.

  14. Evaporative cooling of microscopic water droplets in vacuo: Molecular dynamics simulations and kinetic gas theory.

    Science.gov (United States)

    Schlesinger, Daniel; Sellberg, Jonas A; Nilsson, Anders; Pettersson, Lars G M

    2016-03-28

    In the present study, we investigate the process of evaporative cooling of nanometer-sized droplets in vacuum using molecular dynamics simulations with the TIP4P/2005 water model. The results are compared to the temperature evolution calculated from the Knudsen theory of evaporation which is derived from kinetic gas theory. The calculated and simulation results are found to be in very good agreement for an evaporation coefficient equal to unity. Our results are of interest to experiments utilizing droplet dispensers as well as to cloud micro-physics.

  15. Path-integral molecular dynamics simulations for water anion clusters (HO)5- and (DO)5-

    Science.gov (United States)

    Takayanagi, Toshiyuki; Yoshikawa, Takehiro; Motegi, Haruki; Shiga, Motoyuki

    2009-11-01

    Quantum path-integral molecular dynamics simulations have been performed for the (HO)5- and (DO)5- anion clusters on the basis of a semiempirical one-electron pseudopotential-polarization model. Due to larger zero-point vibrational amplitudes for H atoms than that of D atoms, hydrogen-bond lengths in the (HO)5- cluster are slightly larger than those in (DO)5-. The distribution of the vertical detachment energies for (HO)5- also show a broader feature than that for (DO)5-. The present PIMD simulations thus demonstrate the importance of nuclear quantum effects in water anion clusters.

  16. Molecular dynamics study of ion capture from water by a model ionophore, tetraprotonated cryptand SC24

    Science.gov (United States)

    Owenson, Brian; Macelroy, Robert D.; Pohorille, Andrew

    1988-01-01

    The molecular dynamics of chloride capture from water by the tetraprotonated cryptand SC24 has been studied for the cases of 19 distances between the criptand and the chloride. The chloride capture is found to be characterized by a rapid cooperative change in the conformation of the cryptand when the Cl(-) begins to enter the ligand and just as it encounters the energy barrier. The conformational transition is associated with a shift of three N-H bonds from the pure endo orientation, such that they point toward the chloride.

  17. First principles molecular dynamics of metal/water interfaces under bias potential

    Science.gov (United States)

    Pedroza, Luana; Brandimarte, Pedro; Rocha, Alexandre; Fernandez-Serra, Marivi

    2014-03-01

    Understanding the interaction of the water-metal system at an atomic level is extremely important in electrocatalysts for fuel cells, photocatalysis among other systems. The question of the interface energetics involves a detailed study of the nature of the interactions between water-water and water-substrate. A first principles description of all components of the system is the most appropriate methodology in order to advance understanding of electrochemically processes. In this work we describe, using first principles molecular dynamics simulations, the dynamics of a combined surface(Au and Pd)/water system both in the presence and absence of an external bias potential applied to the electrodes, as one would come across in electrochemistry. This is accomplished using a combination of density functional theory (DFT) and non-equilibrium Green's functions methods (NEGF), thus accounting for the fact that one is dealing with an out-of-equilibrium open system, with and without van der Waals interactions. DOE Early Career Award No. DE-SC0003871.

  18. Cyclo-hexa-peptides at the water/cyclohexane interface: a molecular dynamics simulation.

    Science.gov (United States)

    Cen, Min; Fan, Jian Fen; Liu, Dong Yan; Song, Xue Zeng; Liu, Jian; Zhou, Wei Qun; Xiao, He Ming

    2013-02-01

    Molecular dynamic (MD) simulations have been performed to study the behaviors of ten kinds of cyclo-hexa-peptides (CHPs) composed of amino acids with the diverse hydrophilic/hydrophobic side chains at the water/cyclohexane interface. All the CHPs take the "horse-saddle" conformations at the interface and the hydrophilicity/hydrophobicity of the side chains influences the backbones' structural deformations. The orientations and distributions of the CHPs at the interface and the differences of interaction energies (ΔΔE) between the CHPs and the two liquid phases have been determined. RDF analysis shows that the H-bonds were formed between the O(C) atoms of the CHPs' backbones and H(w) atoms of water molecules. N atoms of the CHPs' backbones formed the H-bonds or van der Waals interactions with the water solvent. It was found that there is a parallel relationship between ΔΔE and the lateral diffusion coefficients (D ( xy )) of the CHPs at the interface. The movements of water molecules close to the interface are confined to some extent, indicating that the dynamics of the CHPs and interfacial water molecules are strongly coupled.

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

    Science.gov (United States)

    Li, Shujuan; Schmidt, Burkhard

    2015-03-21

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

  20. Molecular dynamics simulations of NMR relaxation and diffusion of bulk hydrocarbons and water

    Science.gov (United States)

    Singer, Philip M.; Asthagiri, Dilip; Chapman, Walter G.; Hirasaki, George J.

    2017-04-01

    Molecular dynamics (MD) simulations are used to investigate 1H nuclear magnetic resonance (NMR) relaxation and diffusion of bulk n-C5H12 to n-C17H36 hydrocarbons and bulk water. The MD simulations of the 1H NMR relaxation times T1,2 in the fast motion regime where T1 =T2 agree with measured (de-oxygenated) T2 data at ambient conditions, without any adjustable parameters in the interpretation of the simulation data. Likewise, the translational diffusion DT coefficients calculated using simulation configurations agree with measured diffusion data at ambient conditions. The agreement between the predicted and experimentally measured NMR relaxation times and diffusion coefficient also validate the forcefields used in the simulation. The molecular simulations naturally separate intramolecular from intermolecular dipole-dipole interactions helping bring new insight into the two NMR relaxation mechanisms as a function of molecular chain-length (i.e. carbon number). Comparison of the MD simulation results of the two relaxation mechanisms with traditional hard-sphere models used in interpreting NMR data reveals important limitations in the latter. With increasing chain length, there is substantial deviation in the molecular size inferred on the basis of the radius of gyration from simulation and the fitted hard-sphere radii required to rationalize the relaxation times. This deviation is characteristic of the local nature of the NMR measurement, one that is well-captured by molecular simulations.

  1. Cholesterol effect on water permeability through DPPC and PSM lipid bilayers: a molecular dynamics study.

    Science.gov (United States)

    Saito, Hiroaki; Shinoda, Wataru

    2011-12-29

    Water permeability of two different lipid bilayers of dipalmitoylphosphatidylcholine (DPPC) and palmitoylsphingomyelin (PSM) in the absence and presence of cholesterol (0-50 mol %) have been studied by molecular dynamics simulations to elucidate the molecular mechanism of the reduction in water leakage across the membranes by the addition of cholesterol. An enhanced free energy barrier was observed in these membranes with increased cholesterol concentration, and this was explained by the reduced cavity density around the cholesterol in the hydrophobic membrane core. There was an increase of trans conformers in the hydrophobic lipid chains adjacent to the cholesterol, which reduced the cavity density. The enhanced free energy barrier was found to be the main reason to reduce the water permeability with increased cholesterol concentration. At low cholesterol concentrations the PSM bilayer exhibited a higher free energy barrier than the DPPC bilayer for water permeation, while at greater than 30 mol % of cholesterol the difference became minor. This tendency for the PSM and DPPC bilayers to resemble each other at higher cholesterol concentrations was similar to commonly observed trends in several structural properties, such as order parameters, cross-sectional area per molecule, and cavity density profiles in the hydrophobic regions of bilayer membranes. These results demonstrate that DPPC and PSM bilayers with high cholesterol contents possess similar physical properties, which suggests that the solubility of cholesterol in these lipid bilayers has importance for an understanding of multicomponent lipid membranes with cholesterol.

  2. Structure, dynamics and stability of water/scCO2/mineral interfaces from ab initio molecular dynamics simulations

    Science.gov (United States)

    Lee, Mal-Soon; Peter McGrail, B.; Rousseau, Roger; Glezakou, Vassiliki-Alexandra

    2015-01-01

    The boundary layer at solid-liquid interfaces is a unique reaction environment that poses significant scientific challenges to characterize and understand by experimentation alone. Using ab initio molecular dynamics (AIMD) methods, we report on the structure and dynamics of boundary layer formation, cation mobilization and carbonation under geologic carbon sequestration scenarios (T = 323 K and P = 90 bar) on a prototypical anorthite (001) surface. At low coverage, water film formation is enthalpically favored, but entropically hindered. Simulated adsorption isotherms show that a water monolayer will form even at the low water concentrations of water-saturated scCO2. Carbonation reactions readily occur at electron-rich terminal Oxygen sites adjacent to cation vacancies that readily form in the presence of a water monolayer. These results point to a carbonation mechanism that does not require prior carbonic acid formation in the bulk liquid. This work also highlights the modern capabilities of theoretical methods to address structure and reactivity at interfaces of high chemical complexity. PMID:26456362

  3. Molecular Dynamics of a Water-Absorbent Nanoscale Material Based on Chitosan.

    Science.gov (United States)

    Borca, Carlos H; Arango, Carlos A

    2016-04-21

    Although hydrogels have been widely investigated for their use in materials science, nanotechnology, and novel pharmaceuticals, mechanistic details explaining their water-absorbent features are not well understood. We performed an all-atom molecular dynamics study of the structural transformation of chitosan nanohydrogels due to water absorption. We analyzed the conformation of dry, nanoscaled chitosan, the structural modifications that emerge during the process of water inclusion, and the dynamics of this biopolymer in the presence of nature's solvent. Two sets of nanoscaled, single-chained chitosan models were simulated: one to study the swelling dependence upon the degree of self-cross-linking and other to observe the response with respect to the degree of protonation. We verified that nanohydrogels keep their ability to absorb water and grow, regardless of their degree of cross-linking. Noteworthy, we found that the swelling behavior of nanoscaled chitosan is pH-dependent, and it is considerably more limited than that of larger scale hydrogels. Thus, our study suggests that properties of nanohydrogels are significantly different from those of larger hydrogels. These findings might be important in the design of novel controlled-release and targeted drug-delivery systems based on chitosan.

  4. Effects of Structured Ionomer Interfaces on Water Diffusion: Molecular Dynamics Simulation Insight

    Science.gov (United States)

    Aryal, Dipak; Perahia, Dvora; Grest, Gary

    The dynamics of solvent molecules across structured ionomers interfaces is crucial to innovative technologies with selective controlled transport. These polymers consist of ionizable blocks facilitating transport tethered to mechanical stability enhancing ones, where their incompatibility drives compounded interfaces. Here water penetration through the interface of an A-B-C-B-A co-polymer is probed by atomistic molecular dynamics simulations where C is a randomly sulfonated polystyrene with sulfonation fractions f = 0 to 0.55, B is poly (ethylene-r-propylene) and A is poly (t-butyl styrene). For f>0, a two-step process with slow diffusion at the early stages is observed where water molecules transverse the hydrophobic rich surface before reaching the hydrophilic regime. Water molecules then diffuse along the percolating network of the ionic center block. Increasing the temperature and sulfonation fraction enhances both the rate of diffusion and the overall water uptake. This work is partially supported by DOE: DE-SC007908.

  5. Substructured multibody molecular dynamics.

    Energy Technology Data Exchange (ETDEWEB)

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

    2006-11-01

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

  6. Water radiolysis by low-energy carbon projectiles from first-principles molecular dynamics

    Science.gov (United States)

    Kohanoff, Jorge

    2017-01-01

    Water radiolysis by low-energy carbon projectiles is studied by first-principles molecular dynamics. Carbon projectiles of kinetic energies between 175 eV and 2.8 keV are shot across liquid water. Apart from translational, rotational and vibrational excitation, they produce water dissociation. The most abundant products are H and OH fragments. We find that the maximum spatial production of radiolysis products, not only occurs at low velocities, but also well below the maximum of energy deposition, reaching one H every 5 Å at the lowest speed studied (1 Bohr/fs), dissociative collisions being more significant at low velocity while the amount of energy required to dissociate water is constant and much smaller than the projectile’s energy. A substantial fraction of the energy transferred to fragments, especially for high velocity projectiles, is in the form of kinetic energy, such fragments becoming secondary projectiles themselves. High velocity projectiles give rise to well-defined binary collisions, which should be amenable to binary approximations. This is not the case for lower velocities, where multiple collision events are observed. H secondary projectiles tend to move as radicals at high velocity, as cations when slower. We observe the generation of new species such as hydrogen peroxide and formic acid. The former occurs when an O radical created in the collision process attacks a water molecule at the O site. The latter when the C projectile is completely stopped and reacts with two water molecules. PMID:28267804

  7. Molecular dynamics study of oil detachment from an amorphous silica surface in water medium

    Science.gov (United States)

    Chen, Jiaxuan; Si, Hao; Chen, Wenyang

    2015-10-01

    In this paper, the mechanism of oil detachment from optical glass in water medium is studied by using molecular dynamics simulation. At the beginning, some undecane molecules are adsorbed on the amorphous silica surface to get contaminated glass. Upon addition of 6000 water molecules, most of the undecane molecules on the substrate surface can be detached from an amorphous silica surface through three stages. The formation of different directions of water channels is vital for oil detachment. The electrostatic interaction of water substrate contributes to disturbing the aggregates of undecane molecules and the H-bonding interaction between the water molecules is helpful for the oil puddle away from the substrate. However, there is still some oil molecules residue on the substrate surface after water cleaning. The simulation results showed that the specific ring potential well of amorphous silica surface will hinder the detachment of oil molecules. We also find that the formation of the specific ring potential well is related to the number of atoms and the average radius in silica atomic rings. Increasing the upward lift force, which acts on the hydrocarbon tail of oil molecules, will be benefit to clear the oil pollution residues from the glass surface.

  8. Conserved water molecules in family 1 glycosidases: a DXMS and molecular dynamics study.

    Science.gov (United States)

    Teze, David; Hendrickx, Johann; Dion, Michel; Tellier, Charles; Woods, Virgil L; Tran, Vinh; Sanejouand, Yves-Henri

    2013-08-27

    By taking advantage of the wealth of structural data available for family 1 glycoside hydrolases, a study of the conservation of internal water molecules found in this ubiquitous family of enzymes was undertaken. Strikingly, seven water molecules are observed in more than 90% of the known structures. To gain insight into their possible function, the water dynamics inside Thermus thermophilus β-glycosidase was probed using deuterium exchange mass spectroscopy, allowing the pinpointing of peptide L117-A125, which exchanges most of its amide hydrogens quickly in spite of the fact that it is for the most part buried in the crystal structure. To help interpret this result, a molecular dynamics simulation was performed whose analysis suggests that two water channels are involved in the process. The longest one (∼16 Å) extends between the protein surface and W120, whose side chain interacts with E164 (the acid-base residue involved in the catalytic mechanism), whereas the other channel allows for the exchange with the bulk of the highly conserved water molecules belonging to the hydration shell of D121, a deeply buried residue. Our simulation also shows that another chain of highly conserved water molecules, going from the protein surface to the bottom of the active site cleft close to the nucleophile residue involved in the catalytic mechanism, is able to exchange with the bulk on the nanosecond time scale. It is tempting to speculate that at least one of these three water channels could be involved in the function of family 1 glycoside hydrolases.

  9. Interaction of the model alkyltrimethylammonium ions with alkali halide salts: an explicit water molecular dynamics study

    Directory of Open Access Journals (Sweden)

    M. Druchok

    2013-01-01

    Full Text Available We present an explicit water molecular dynamics simulation of dilute solutions of model alkyltrimethylammonium surfactant ions (number of methylene groups in the tail is 3, 5, 8, 10, and 12 in mixture with NaF, NaCl, NaBr, and NaI salts, respectively. The SPC/E model is used to describe water molecules. Results of the simulation at 298 K are presented in form of the radial distribution functions between nitrogen and carbon atoms of CH2 groups on the alkyltrimethylammonium ion, and the counterion species in the solution. The running coordination numbers between carbon atoms of surfactants and counterions are also calculated. We show that I- counterion exhibits the highest, and F- the lowest affinity to "bind" to the model surfactants. The results are discussed in view of the available experimental and simulation data for this and similar solutions.

  10. Labyrinthine water flow across multilayer graphene-based membranes: molecular dynamics versus continuum predictions

    CERN Document Server

    Yoshida, Hiroaki

    2016-01-01

    In this paper we investigate the hydrodynamic permeance of water through graphene-based membranes, inspired by recent experimental findings on graphene-oxide membranes. We consider the flow across multiple graphene layers having nanoslits in a staggered alignment, with an inter-layer distance ranging from sub- nanometer to a few nanometers. We compare results for the permeability obtained by means of molecular dynamics simulations to continuum predictions obtained by using the lattice Boltzmann calculations and hydrodynamic modelization. This highlights that, in spite of extreme confinement, the permeability across the graphene-based membrane is quantitatively predicted on the basis of a continuum expression, taking properly into account entrance and slippage effects of the confined water flow. Our predictions refute the breakdown of hydrodynamics at small scales in these membrane systems. They constitute a benchmark to which we compare published experimental data.

  11. Proton momentum distributions in water: A path integral molecular dynamics study

    Science.gov (United States)

    Srinivasan, Varadharajan; Morrone, Joseph A.; Sebastiani, Daniel; Car, Roberto

    2007-03-01

    Recent neutron Compton scattering experiments have detected the proton momentum distributions of water. This density in momentum space is a quantum mechanical property of the proton, due to the confining anharmonic potential from covalent and hydrogen bonds. The theoretical calculation of this property can be carried out via ``open'' path integral expressions. In this work, we present an extension of the staging path integral molecular dynamics method, which is then employed to calculate the proton momentum distributions of water in the solid, liquid, and supercritical phases. We utilize the SPC/F2 empirical force field to model the system's interactions. The calculated momentum distributions depict both agreement and discrepancies with experiment. The differences may be explained by the deviation of the force field from the true interactions. These distributions provide an abundance of information about the environment and interactions surrounding the proton.

  12. Proton momentum distribution in water: an open path integral molecular dynamics study

    Science.gov (United States)

    Morrone, Joseph A.; Srinivasan, Varadharajan; Sebastiani, Daniel; Car, Roberto

    2007-06-01

    Recent neutron Compton scattering experiments have detected the proton momentum distribution in water. The theoretical calculation of this property can be carried out via "open" path integral expressions. In this work, present an extension of the staging path integral molecular dynamics method, which is then employed to calculate the proton momentum distributions of water in the solid, liquid, and supercritical phases. We utilize a flexible, single point charge empirical force field to model the system's interactions. The calculated momentum distributions depict both agreement and discrepancies with experiment. The differences may be explained by the deviation of the force field from the true interactions. These distributions provide an abundance of information about the environment and interactions surrounding the proton.

  13. Ab initio molecular dynamics simulation of liquid water by quantum Monte Carlo

    Energy Technology Data Exchange (ETDEWEB)

    Zen, Andrea, E-mail: a.zen@ucl.ac.uk [Dipartimento di Fisica, “La Sapienza” - Università di Roma, piazzale Aldo Moro 5, 00185 Rome (Italy); London Centre for Nanotechnology, University College London, London WC1E 6BT (United Kingdom); Luo, Ye, E-mail: xw111luoye@gmail.com; Mazzola, Guglielmo, E-mail: gmazzola@phys.ethz.ch; Sorella, Sandro, E-mail: sorella@sissa.it [SISSA–International School for Advanced Studies, Via Bonomea 26, 34136 Trieste (Italy); Democritos Simulation Center CNR–IOM Istituto Officina dei Materiali, 34151 Trieste (Italy); Guidoni, Leonardo, E-mail: leonardo.guidoni@univaq.it [Dipartimento di Fisica, “La Sapienza” - Università di Roma, piazzale Aldo Moro 5, 00185 Rome (Italy); Dipartimento di Scienze Fisiche e Chimiche, Università degli Studi dell’ Aquila, via Vetoio, 67100 L’ Aquila (Italy)

    2015-04-14

    Although liquid water is ubiquitous in chemical reactions at roots of life and climate on the earth, the prediction of its properties by high-level ab initio molecular dynamics simulations still represents a formidable task for quantum chemistry. In this article, we present a room temperature simulation of liquid water based on the potential energy surface obtained by a many-body wave function through quantum Monte Carlo (QMC) methods. The simulated properties are in good agreement with recent neutron scattering and X-ray experiments, particularly concerning the position of the oxygen-oxygen peak in the radial distribution function, at variance of previous density functional theory attempts. Given the excellent performances of QMC on large scale supercomputers, this work opens new perspectives for predictive and reliable ab initio simulations of complex chemical systems.

  14. Ab-initio molecular dynamics simulation of liquid water by Quantum Monte Carlo

    CERN Document Server

    Zen, Andrea; Mazzola, Guglielmo; Guidoni, Leonardo; Sorella, Sandro

    2014-01-01

    Despite liquid water is ubiquitous in chemical reactions at roots of life and climate on earth, the prediction of its properties by high-level ab initio molecular dynamics simulations still represents a formidable task for quantum chemistry. In this article we present a room temperature simulation of liquid water based on the potential energy surface obtained by a many-body wave function through quantum Monte Carlo (QMC) methods. The simulated properties are in excellent agreement with recent neutron scattering and X-ray experiments, particularly concerning the position of the oxygen-oxygen peak in the radial distribution function, at variance of previous Density Functional Theory attempts. Given the excellent performances of QMC on large scale supercomputers, this work opens new perspectives for predictive and reliable ab-initio simulations of complex chemical systems.

  15. Development of EEM based silicon–water and silica–water wall potentials for non-reactive molecular dynamics simulations

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Junghan; Iype, Eldhose; Frijns, Arjan J.H.; Nedea, Silvia V.; Steenhoven, Anton A. van

    2014-07-01

    Molecular dynamics simulations of heat transfer in gases are computationally expensive when the wall molecules are explicitly modeled. To save computational time, an implicit boundary function is often used. Steele's potential has been used in studies of fluid–solid interface for a long time. In this work, the conceptual idea of Steele's potential was extended in order to simulate water–silicon and water–silica interfaces. A new wall potential model is developed by using the electronegativity-equalization method (EEM), a ReaxFF empirical force field and a non-reactive molecular dynamics package PumMa. Contact angle simulations were performed in order to validate the wall potential model. Contact angle simulations with the resulting tabulated wall potentials gave a silicon–water contact angle of 129°, a quartz–water contact angle of 0°, and a cristobalite–water contact angle of 40°, which are in reasonable agreement with experimental values.

  16. Quantify Water Extraction by TBP/Dodecane via Molecular Dynamics Simulations

    Energy Technology Data Exchange (ETDEWEB)

    Khomami, Bamin [Univ. of Tennessee, Knoxville, TN (United States); Cui, Shengting [Univ. of Tennessee, Knoxville, TN (United States); de Almeida, Valmor F. [Oak Ridge National Lab., Oak Ridge, TN (United States); Felker, Kevin [Oak Ridge National Lab., Oak Ridge, TN (United States)

    2013-05-16

    The purpose of this project is to quantify the interfacial transport of water into the most prevalent nuclear reprocessing solvent extractant mixture, namely tri-butyl- phosphate (TBP) and dodecane, via massively parallel molecular dynamics simulations on the most powerful machines available for open research. Specifically, we will accomplish this objective by evolving the water/TBP/dodecane system up to 1 ms elapsed time, and validate the simulation results by direct comparison with experimentally measured water solubility in the organic phase. The significance of this effort is to demonstrate for the first time that the combination of emerging simulation tools and state-of-the-art supercomputers can provide quantitative information on par to experimental measurements for solvent extraction systems of relevance to the nuclear fuel cycle. Results: Initially, the isolated single component, and single phase systems were studied followed by the two-phase, multicomponent counterpart. Specifically, the systems we studied were: pure TBP; pure n-dodecane; TBP/n-dodecane mixture; and the complete extraction system: water-TBP/n-dodecane two phase system to gain deep insight into the water extraction process. We have completely achieved our goal of simulating the molecular extraction of water molecules into the TBP/n-dodecane mixture up to the saturation point, and obtained favorable comparison with experimental data. Many insights into fundamental molecular level processes and physics were obtained from the process. Most importantly, we found that the dipole moment of the extracting agent is crucially important in affecting the interface roughness and the extraction rate of water molecules into the organic phase. In addition, we have identified shortcomings in the existing OPLS-AA force field potential for long-chain alkanes. The significance of this force field is that it is supposed to be optimized for molecular liquid simulations. We found that it failed for dodecane and

  17. Molecular dynamics of a tetrasaccharide subunit of chondroitin 4-sulfate in water.

    Science.gov (United States)

    Kaufmann, J; Möhle, K; Hofmann, H J; Arnold, K

    1999-05-31

    Molecular dynamics (MD) simulations on a tetrasaccharide subunit of chondroitin 4-sulfate (CS4) in aqueous solution were carried out to study its interactions with water. Pair distribution functions and diffusion coefficients were calculated from a 4 ns trajectory and the hydration of different molecular groups was analysed. The average values of the interglycosidic torsion angles found in the simulations are phi 13 = -10 degrees, psi 13 = -85 degrees and phi 13 = 80 degrees, psi 13 = 90 degrees for the beta-(1-->3) linkage, and phi 14 = -10 degrees, psi 14 = -70 degrees for the beta-(1-->4) linkage. Hydrophobic patches formed by sugar ring CH groups were found. The diffusion coefficients of the water molecules vary from 1.4 x 10(-9) to 2.3 x 10(-9) m2 s-1 depending on the distances between the water molecules and the atoms of the CS4 molecule and the type of CS4 atoms, respectively. Reorientation correlation times of the water molecules in the vicinity of different CS4 atoms were estimated to be about 1 ps at a polymer concentration of 4 wt.% CS4. The number of hydrogen bonds between the water molecules and the acceptor atoms of CS4 was determined to be about 20 per disaccharide unit, indicating a higher hydration ability of chondroitin sulfate in comparison with non-sulfated oligosaccharides. Substructures, where water molecules are involved in hydrogen bonds to different sugar rings, were found, which may be important for the stabilisation of the secondary structure of the CS4 molecule.

  18. The Aqueous Solvation of Water A Comparison of Continuum Methods with Molecular Dynamics

    CERN Document Server

    Rick, S W; Rick, Steven W.

    1994-01-01

    The calculation of the solvation properties of a single water molecule in liquid water is carried out in two ways. In the first, the water molecule is placed in a cavity and the solvent is treated as a dielectric continuum. This model is analyzed by numerically solving the Poisson equation using the DelPhi program. The resulting solvation properties depend sensitively on the shape and size of the cavity. In the second method, the solvent and solute molecules are treated explicitly in molecular dynamics simulations using Ewald boundary conditions. We find a 2 kcal/mole difference in solvation free energies predicted by these two methods when standard cavity radii are used. In addition, dielectric continuum theory assumes that the solvent reacts solely by realigning its electric moments linearly with the strength of the solute's electric field; the results of the molecular simulation show important non-linear effects. Non-linear solvent effects are generally of two types: dielectric saturation, due to solvent-s...

  19. Hydroxyl and water molecule orientations in trypsin: Comparison to molecular dynamics structures

    Energy Technology Data Exchange (ETDEWEB)

    McDowell, R.S.; Kossiakoff, A.A. [Genentech, Inc., South San Francisco, CA (United States)

    1994-12-31

    A comparison is presented of experimentally observed hydroxyl and water hydrogens in trypsin determined from neutron density maps with the results of a 140ps molecular dynamics (MD) simulation. Experimental determination of hydrogen and deuterium atom positions in molecules as large as proteins is a unique capability of neutron diffraction. The comparison addresses the degree to which a standard force-field approach can adequately describe the local electrostatic and van der Waals forces that determine the orientations of these hydrogens. Neutron densities, derived from 2.1{Angstrom} D{sub 2}O-H{sub 2}O difference Fourier maps, provide a database of 27 well-ordered hydroxyl hydrogens. Most of the simulated hydroxyl orientations are within a standard deviation of the experimentally-observed positions, including several examples in which both the simulation and the neutron density indicate that a hydroxyl group is shifted from a {open_quote}standard{close_quote} rotamer. For the most highly ordered water molecules, the hydrogen distributions calculated from the trajectory were in good agreement with neutron density; simulated water molecules that displayed multiple hydrogen bonding networks had correspondingly broadened neutron density profiles. This comparison was facilitated by development of a method to construct a pseudo 2{Angstrom} density map based on the hydrogen atom distributions from the simulation. The degree of disorder of internal water molecules is shown to result primarily from the electrostatic environment surrounding that water molecule as opposed to the cavity size available to the molecule. A method is presented for comparing the discrete observations sampled in a dynamics trajectory with the time- averaged data obtained from X-ray or neutron diffraction studies. This method is particularly useful for statically-disordered water molecules, in which the average location assigned from a trajectory may represent a site of relatively low occupancy.

  20. Molecular dynamics simulations of the ice temperature dependence of water ice photodesorption

    CERN Document Server

    Arasa, C; Cuppen, H M; van Dishoweck, E F; Kroes, G -J; 10.1063/1.3422213

    2010-01-01

    The ultraviolet (UV) photodissociation of amorphous water ice at different ice temperatures is investigated using molecular dynamics (MD) simulations and analytical potentials. Previous MD calculations of UV photodissociation of amorphous and crystalline water ice at 10 K [S. Andersson et al., J. Chem. Phys. 124, 064715 (2006)] revealed -for both types of ice- that H atom, OH, and H2O desorption are the most important processes after photoexcitation in the uppermost layers of the ice. Water desorption takes place either by direct desorption of recombined water, or when, after dissociation, an H atom transfers part of its kinetic energy to one of the surrounding water molecules which is thereby kicked out from the ice. We present results of MD simulations of UV photodissociation of amorphous ice at 10, 20, 30, and 90 K in order to analyze the effect of ice temperature on UV photodissociation processes. Desorption and trapping probabilities are calculated for photoexcitation of H2O in the top four monolayers an...

  1. Investigating the quartz (1010)/water interface using classical and ab initio molecular dynamics.

    Science.gov (United States)

    Skelton, A A; Wesolowski, D J; Cummings, P T

    2011-07-19

    Two different terminations of the (1010) surface of quartz (α and β) interacting with water are simulated by classical (CMD) (using two different force fields) and ab initio molecular dynamics (AIMD) and compared with previously published X-ray reflectivity (XR) experiments. Radial distribution functions between hydroxyl and water show good agreement between AIMD and CMD using the ClayFF force field for both terminations. The Lopes et al. (Lopes, P. E. M.; Murashov, V.; Tazi, M.; Demchuk, E.; MacKerell, A. D. J. Phys. Chem. B2006, 110, 2782-2792) force field (LFF), however, underestimates the extent of hydroxyl-water hydrogen bonding. The β termination is found to contain hydroxyl-hydroxyl hydrogen bonds; the quartz surface hydroxyl hydrogens and oxygens that hydrogen bond with each other exhibit greatly reduced hydrogen bonding to water. Conversely, the hydroxyl hydrogen and oxygens that are not hydrogen bonded to other surface hydroxyls but are connected to those that are show a considerable amount of hydrogen bonding to water. The electron density distribution of an annealed surface of quartz (1010) obtained by XR is in qualitative agreement with electron densities calculated by CMD and AIMD. In all simulation methods, the interfacial water peak appears farther from the surface than observed by XR. Agreement among AIMD, LFF, and XR is observed for the relaxation of the near-surface atoms; however, ClayFF shows a larger discrepancy. Overall, results show that for both terminations of (1010), LFF treats the near-surface structure more accurately whereas ClayFF treats the interfacial water structure more accurately. It is shown that the number of hydroxyl and water hydrogen bonds to the bridging Si-O-Si oxygens connecting the surface silica groups to the rest of the crystal is much greater for the α than the β termination. It is suggested that this may play a role in the greater resistance to dissolution of the β termination than that of the α termination.

  2. A molecular dynamics implementation of the 3D Mercedes-Benz water model

    Science.gov (United States)

    Hynninen, T.; Dias, C. L.; Mkrtchyan, A.; Heinonen, V.; Karttunen, M.; Foster, A. S.; Ala-Nissila, T.

    2012-02-01

    The three-dimensional Mercedes-Benz model was recently introduced to account for the structural and thermodynamic properties of water. It treats water molecules as point-like particles with four dangling bonds in tetrahedral coordination, representing H-bonds of water. Its conceptual simplicity renders the model attractive in studies where complex behaviors emerge from H-bond interactions in water, e.g., the hydrophobic effect. A molecular dynamics (MD) implementation of the model is non-trivial and we outline here the mathematical framework of its force-field. Useful routines written in modern Fortran are also provided. This open source code is free and can easily be modified to account for different physical context. The provided code allows both serial and MPI-parallelized execution. Program summaryProgram title: CASHEW (Coarse Approach Simulator for Hydrogen-bonding Effects in Water) Catalogue identifier: AEKM_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEKM_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 20 501 No. of bytes in distributed program, including test data, etc.: 551 044 Distribution format: tar.gz Programming language: Fortran 90 Computer: Program has been tested on desktop workstations and a Cray XT4/XT5 supercomputer. Operating system: Linux, Unix, OS X Has the code been vectorized or parallelized?: The code has been parallelized using MPI. RAM: Depends on size of system, about 5 MB for 1500 molecules. Classification: 7.7 External routines: A random number generator, Mersenne Twister ( http://www.math.sci.hiroshima-u.ac.jp/m-mat/MT/VERSIONS/FORTRAN/mt95.f90), is used. A copy of the code is included in the distribution. Nature of problem: Molecular dynamics simulation of a new geometric water model. Solution method: New force-field for

  3. Dynamical properties of liquid water from ab initio molecular dynamics performed in the complete basis set limit

    Science.gov (United States)

    Lee, Hee-Seung; Tuckerman, Mark E.

    2007-04-01

    Dynamical properties of liquid water were studied using Car-Parrinello [Phys. Rev. Lett. 55, 2471 (1985)] ab initio molecular dynamics (AIMD) simulations within the Kohn-Sham (KS) density functional theory employing the Becke-Lee-Yang-Parr exchange-correlation functional for the electronic structure. The KS orbitals were expanded in a discrete variable representation basis set, wherein the complete basis set limit can be easily reached and which, therefore, provides complete convergence of ionic forces. In order to minimize possible nonergodic behavior of the simulated water system in a constant energy (NVE) ensemble, a long equilibration run (30ps) preceded a 60ps long production run. The temperature drift during the entire 60ps trajectory was found to be minimal. The diffusion coefficient [0.055Å2/ps] obtained from the present work for 32 D2O molecules is a factor of 4 smaller than the most up to date experimental value, but significantly larger than those of other recent AIMD studies. Adjusting the experimental result so as to match the finite-sized system used in the present study brings the comparison between theory and experiment to within a factor of 3. More importantly, the system is not observed to become "glassy" as has been reported in previous AIMD studies. The computed infrared spectrum is in good agreement with experimental data, especially in the low frequency regime where the translational and librational motions of water are manifested. The long simulation length also made it possible to perform detailed studies of hydrogen bond dynamics. The relaxation dynamics of hydrogen bonds observed in the present AIMD simulation is slower than those of popular force fields, such as the TIP4P potential, but comparable to that of the TIP5P potential.

  4. Molecular dynamic simulations of iron (II) hydroxide in high temperature and supercritical water

    Science.gov (United States)

    Meng, Yuanliang

    In this study, the iron (II) hydroxide -- water system has been investigated at high temperatures by using molecular dynamics (MD) simulations. The simulation results reveal that at infinite dilution both Fe2+ cation and OH- anion have 6 water molecules within their first hydration shell and both types of ionic species experience a dramatic increase in their diffusion coefficients at near and supercritical conditions. The process of iron (II) hydroxide cluster formation has been simulated. The nano-clusters of larger sizes formed in supercritical water tend to be in an amorphous state. After having been quenched by an inert gas bath, iron (II) hydroxide nano-clusters with various structures have been produced. The geometries and associated binding energies of these species are given in detail. The vibrational spectra of iron (II) hydroxide clusters are also derived and compared with the spectrum of a bulk solid. The obtained results have a practical value for the analysis of potential corrosion products in supercritical water-cooled reactor (SCWR) which is employed in the new generation nuclear power plant design (GEN IV). This work also illustrates the process of hydrothermal synthesis of oxide nano-particles.

  5. Wetting and evaporation of salt-water nanodroplets: A molecular dynamics investigation

    Science.gov (United States)

    Zhang, Jun; Borg, Matthew K.; Sefiane, Khellil; Reese, Jason M.

    2015-11-01

    We employ molecular dynamics simulations to study the wetting and evaporation of salt-water nanodroplets on platinum surfaces. Our results show that the contact angle of the droplets increases with the salt concentration. To verify this, a second simulation system of a thin salt-water film on a platinum surface is used to calculate the various surface tensions. We find that both the solid-liquid and liquid-vapor surface tensions increase with salt concentration and as a result these cause an increase in the contact angle. However, the evaporation rate of salt-water droplets decreases as the salt concentration increases, due to the hydration of salt ions. When the water molecules have all evaporated from the droplet, two forms of salt crystals are deposited, clump and ringlike, depending on the solid-liquid interaction strength and the evaporation rate. To form salt crystals in a ring, it is crucial that there is a pinned stage in the evaporation process, during which salt ions can move from the center to the rim of the droplets. With a stronger solid-liquid interaction strength, a slower evaporation rate, and a higher salt concentration, a complete salt crystal ring can be deposited on the surface.

  6. Wetting and evaporation of salt-water nanodroplets: A molecular dynamics investigation.

    Science.gov (United States)

    Zhang, Jun; Borg, Matthew K; Sefiane, Khellil; Reese, Jason M

    2015-11-01

    We employ molecular dynamics simulations to study the wetting and evaporation of salt-water nanodroplets on platinum surfaces. Our results show that the contact angle of the droplets increases with the salt concentration. To verify this, a second simulation system of a thin salt-water film on a platinum surface is used to calculate the various surface tensions. We find that both the solid-liquid and liquid-vapor surface tensions increase with salt concentration and as a result these cause an increase in the contact angle. However, the evaporation rate of salt-water droplets decreases as the salt concentration increases, due to the hydration of salt ions. When the water molecules have all evaporated from the droplet, two forms of salt crystals are deposited, clump and ringlike, depending on the solid-liquid interaction strength and the evaporation rate. To form salt crystals in a ring, it is crucial that there is a pinned stage in the evaporation process, during which salt ions can move from the center to the rim of the droplets. With a stronger solid-liquid interaction strength, a slower evaporation rate, and a higher salt concentration, a complete salt crystal ring can be deposited on the surface.

  7. A Comprehensive Study of Hydrogen Adsorbing to Amorphous Water ice: Defining Adsorption in Classical Molecular Dynamics

    Science.gov (United States)

    Dupuy, John L.; Lewis, Steven P.; Stancil, P. C.

    2016-11-01

    Gas-grain and gas-phase reactions dominate the formation of molecules in the interstellar medium (ISM). Gas-grain reactions require a substrate (e.g., a dust or ice grain) on which the reaction is able to occur. The formation of molecular hydrogen (H2) in the ISM is the prototypical example of a gas-grain reaction. In these reactions, an atom of hydrogen will strike a surface, stick to it, and diffuse across it. When it encounters another adsorbed hydrogen atom, the two can react to form molecular hydrogen and then be ejected from the surface by the energy released in the reaction. We perform in-depth classical molecular dynamics simulations of hydrogen atoms interacting with an amorphous water-ice surface. This study focuses on the first step in the formation process; the sticking of the hydrogen atom to the substrate. We find that careful attention must be paid in dealing with the ambiguities in defining a sticking event. The technical definition of a sticking event will affect the computed sticking probabilities and coefficients. Here, using our new definition of a sticking event, we report sticking probabilities and sticking coefficients for nine different incident kinetic energies of hydrogen atoms [5-400 K] across seven different temperatures of dust grains [10-70 K]. We find that probabilities and coefficients vary both as a function of grain temperature and incident kinetic energy over the range of 0.99-0.22.

  8. Molecular Dynamics Simulations of CO2/Water/Quartz Interfacial Properties: Impact of CO2 Dissolution in Water.

    Science.gov (United States)

    Javanbakht, Gina; Sedghi, Mohammad; Welch, William; Goual, Lamia

    2015-06-01

    The safe trapping of carbon dioxide (CO2) in deep saline aquifers is one of the major concerns of CO2 sequestration. The amount of capillary trapping is dominated by the capillary pressure of water and CO2 inside the reservoir, which in turn is controlled by the interfacial tension (IFT) and the contact angle (CA) of CO2/water/rock systems. The measurement of IFT and CA could be very challenging at reservoir conditions, especially in the presence of toxic cocontaminants. Thus, the ability to accurately predict these interfacial properties at reservoir conditions is very advantageous. Although the majority of existing molecular dynamics (MD) studies of CO2/water/mineral systems were able to capture the trends in IFT and CA variations with pressure and temperature, their predictions often deviated from experimental data, possibly due to erroneous models and/or overlooked chemical reactions. The objective of this study was to improve the MD predictions of IFT and CA of CO2/water/quartz systems at various pressure and temperature conditions by (i) considering the chemical reactions between CO2 and water and (ii) using a new molecular model for α-quartz surface. The results showed that the presence of carbonic acid at the CO2/water interface improved the predictions of IFT, especially at low temperature and high pressure where more CO2 dissolution occurs. On the other hand, the effect on CA was minor. The slight decrease in CA observed across the pressure range investigated could be attributed to an increase in the total number of H-bonds between fluid molecules and quartz surface.

  9. Hydration and translocation of an excess proton in water clusters: An ab initio molecular dynamics study

    Indian Academy of Sciences (India)

    Arindam Bankura; Amalendu Chandra

    2005-10-01

    The hydration structure and translocation of an excess proton in hydrogen bonded water clusters of two different sizes are investigated by means of finite temperature quantum simulations. The simulations are performed by employing the method of Car–Parrinello molecular dynamics where the forces on the nuclei are obtained directly from `on the fly' quantum electronic structure calculations. Since no predefined interaction potentials are used in this scheme, it is ideally suited to study proton translocation processes which proceed through breaking and formation of chemical bonds. The coordination number of the hydrated proton and the index of oxygen to which the excess proton is attached are calculated along the simulation trajectories for both the clusters.

  10. Molecular dynamics simulations of the contact angle between water droplets and graphite surfaces

    CERN Document Server

    Sergi, Danilo; Ortona, Alberto

    2012-01-01

    Wetting is a widespread phenomenon, most prominent in a number of cases, both in nature and technology. Droplets of pure water with initial radius ranging from 20 to 80 [\\AA] spreading on graphitic surfaces are studied by molecular dynamics simulations. The equilibrium contact angle is determined and the transition to the macroscopic limit is discussed using Young equation in its modified form. While the largest droplets are almost perfectly spherical, the profiles of the smallest ones are no more properly described by a circle. For the sake of accuracy, we employ a more general fitting procedure based on local linear regressions. Furthermore, our results reveal that there is a possible transition to the macroscopic limit. The modified Young equation is particularly precise for characteristic lengths (radii and contact-line curvatures) around 40 [\\AA].

  11. High density gas state at water/graphite interface studied by molecular dynamics simulation

    Institute of Scientific and Technical Information of China (English)

    Wang Chun-Lei; Li Zhao-Xia; Li Jing-Yuan; Xiu Peng; Hu Jun; Fang Hai-Ping

    2008-01-01

    In this paper molecular dynamics simulations are performed to study the accumulation behaviour of N2 and H2 at water/graphite interface under ambient temperature and pressure. It finds that both N2 and H2 molecules can accumulate at the interface and form one of two states according to the ratio of gas molecules number to square of graphite surface from our simulation results: gas films (pancake-like) for a larger ratio and nanobubbles for a Smaller ratio. In addition, we discuss the stabilities of nanobubbles at different environment temperatures. Surprisingly, it is found that the density of both kinds of gas states can be greatly increased, even comparable with that of the liquid N2 and liquid H2. The present results are expected to be helpful for the understanding of the stable existence of gas film (pancake-like) and nanobubbles.

  12. Revisiting Molecular Dynamics on a CPU/GPU system: Water Kernel and SHAKE Parallelization.

    Science.gov (United States)

    Ruymgaart, A Peter; Elber, Ron

    2012-11-13

    We report Graphics Processing Unit (GPU) and Open-MP parallel implementations of water-specific force calculations and of bond constraints for use in Molecular Dynamics simulations. We focus on a typical laboratory computing-environment in which a CPU with a few cores is attached to a GPU. We discuss in detail the design of the code and we illustrate performance comparable to highly optimized codes such as GROMACS. Beside speed our code shows excellent energy conservation. Utilization of water-specific lists allows the efficient calculations of non-bonded interactions that include water molecules and results in a speed-up factor of more than 40 on the GPU compared to code optimized on a single CPU core for systems larger than 20,000 atoms. This is up four-fold from a factor of 10 reported in our initial GPU implementation that did not include a water-specific code. Another optimization is the implementation of constrained dynamics entirely on the GPU. The routine, which enforces constraints of all bonds, runs in parallel on multiple Open-MP cores or entirely on the GPU. It is based on Conjugate Gradient solution of the Lagrange multipliers (CG SHAKE). The GPU implementation is partially in double precision and requires no communication with the CPU during the execution of the SHAKE algorithm. The (parallel) implementation of SHAKE allows an increase of the time step to 2.0fs while maintaining excellent energy conservation. Interestingly, CG SHAKE is faster than the usual bond relaxation algorithm even on a single core if high accuracy is expected. The significant speedup of the optimized components transfers the computational bottleneck of the MD calculation to the reciprocal part of Particle Mesh Ewald (PME).

  13. Equilibrium fractionation of H and O isotopes in water from path integral molecular dynamics

    Science.gov (United States)

    Pinilla, Carlos; Blanchard, Marc; Balan, Etienne; Ferlat, Guillaume; Vuilleumier, Rodolphe; Mauri, Francesco

    2014-06-01

    The equilibrium fractionation factor between two phases is of importance for the understanding of many planetary and environmental processes. Although thermodynamic equilibrium can be achieved between minerals at high temperature, many natural processes involve reactions between liquids or aqueous solutions and solids. For crystals, the fractionation factor α can be theoretically determined using a statistical thermodynamic approach based on the vibrational properties of the phases. These calculations are mostly performed in the harmonic approximation, using empirical or ab-initio force fields. In the case of aperiodic and dynamic systems such as liquids or solutions, similar calculations can be done using finite-size molecular clusters or snapshots obtained from molecular dynamics (MD) runs. It is however difficult to assess the effect of these approximate models on the isotopic fractionation properties. In this work we present a systematic study of the calculation of the D/H and 18O/16O equilibrium fractionation factors in water for the liquid/vapour and ice/vapour phases using several levels of theory within the simulations. Namely, we use a thermodynamic integration approach based on Path Integral MD calculations (PIMD) and an empirical potential model of water. Compared with standard MD, PIMD takes into account quantum effects in the thermodynamic modeling of systems and the exact fractionation factor for a given potential can be obtained. We compare these exact results with those of modeling strategies usually used, which involve the mapping of the quantum system on its harmonic counterpart. The results show the importance of including configurational disorder for the estimation of isotope fractionation in liquid phases. In addition, the convergence of the fractionation factor as a function of parameters such as the size of the simulated system and multiple isotope substitution is analyzed, showing that isotope fractionation is essentially a local effect in

  14. Predict the glass transition temperature of glycerol-water binary cryoprotectant by molecular dynamic simulation.

    Science.gov (United States)

    Li, Dai-Xi; Liu, Bao-Lin; Liu, Yi-shu; Chen, Cheng-lung

    2008-04-01

    Vitrification is proposed to be the best way for the cryopreservation of organs. The glass transition temperature (T(g)) of vitrification solutions is a critical parameter of fundamental importance for cryopreservation by vitrification. The instruments that can detect the thermodynamic, mechanical and dielectric changes of a substance may be used to determine the glass transition temperature. T(g) is usually measured by using differential scanning calorimetry (DSC). In this study, the T(g) of the glycerol-aqueous solution (60%, wt/%) was determined by isothermal-isobaric molecular dynamic simulation (NPT-MD). The software package Discover in Material Studio with the Polymer Consortium Force Field (PCFF) was used for the simulation. The state parameters of heat capacity at constant pressure (C(p)), density (rho), amorphous cell volume (V(cell)) and specific volume (V(specific)) and radial distribution function (rdf) were obtained by NPT-MD in the temperature range of 90-270K. These parameters showed a discontinuity at a specific temperature in the plot of state parameter versus temperature. The temperature at the discontinuity is taken as the simulated T(g) value for glycerol-water binary solution. The T(g) values determined by simulation method were compared with the values in the literatures. The simulation values of T(g) (160.06-167.51K) agree well with the DSC results (163.60-167.10K) and the DMA results (159.00K). We drew the conclusion that molecular dynamic simulation (MDS) is a potential method for investigating the glass transition temperature (T(g)) of glycerol-water binary cryoprotectants and may be used for other vitrification solutions.

  15. Adsorption and solvation of ethanol at the water liquid-vapor interface: a molecular dynamics study

    Science.gov (United States)

    Wilson, M. A.; Pohorille, A.

    1997-01-01

    The free energy profiles of methanol and ethanol at the water liquid-vapor interface at 310K were calculated using molecular dynamics computer simulations. Both alcohols exhibit a pronounced free energy minimum at the interface and, therefore, have positive adsorption at this interface. The surface excess was computed from the Gibbs adsorption isotherm and was found to be in good agreement with experimental results. Neither compound exhibits a free energy barrier between the bulk and the surface adsorbed state. Scattering calculations of ethanol molecules from a gas phase thermal distribution indicate that the mass accommodation coefficient is 0.98, and the molecules become thermalized within 10 ps of striking the interface. It was determined that the formation of the solvation structure around the ethanol molecule at the interface is not the rate-determining step in its uptake into water droplets. The motion of an ethanol molecule in a water lamella was followed for 30 ns. The time evolution of the probability distribution of finding an ethanol molecule that was initially located at the interface is very well described by the diffusion equation on the free energy surface.

  16. Geometric isotope effects on small chloride ion water clusters with path integral molecular dynamics simulations

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Qi [Department of Chemistry, Tsukuba University, 1-1-1 Tennodai, Tsukuba 305-8571 (Japan); Suzuki, Kimichi [Research Institute for Nanosystem, National Institute of Advanced Industrial Science and Technology, Chuo-2, 1-1-1 Umezono, Tsukuba, Ibaraki 305-8568 (Japan); Nagashima, Umpei, E-mail: u.nagashima@aist.go.jp [Department of Chemistry, Tsukuba University, 1-1-1 Tennodai, Tsukuba 305-8571 (Japan); Research Institute for Nanosystem, National Institute of Advanced Industrial Science and Technology, Chuo-2, 1-1-1 Umezono, Tsukuba, Ibaraki 305-8568 (Japan); Tachikawa, Masanori [Quantum Chemistry Division, Graduate School of Science, Yokohama-City University, Seto 22-2, Kanazawa-ku, Yokohama 236-0027 (Japan); Yan, Shiwei [College of Nuclear Science and Technology, Beijing Normal University, Beijing 100875 (China)

    2013-11-29

    Highlights: • PIMD simulations with PM6-DH+ potential are carried out for Cl{sup −}(H{sub 2}O){sub n} clusters. • The geometric isotope effects on the rearrangement of single and multi shell structures are presented. • The competition of intramolecular and intermolecular nuclear quantum effects on the cluster structures is shown. • The correlations between r(Cl…O) and other vibration motions are discussed. - Abstract: The geometric isotope effects on the structures of hydrated chloride ionic hydrogen bonded clusters are explored by carrying out path integral molecular dynamics simulations. First, an outer shell coordinate is selected to display the rearrangement of single and multi hydration shell cluster structures. Next, to show the competition of intramolecular and intermolecular nuclear quantum effects, the intramolecular OH{sup ∗} stretching and intermolecular ion–water wagging motions are studied for single and multi shell structures, respectively. The results indicate that the intermolecular nuclear quantum effects stabilize the ionic hydrogen bonds in single shell structures, while they are destabilized through the competition with intramolecular nuclear quantum effects in multi shell structures. In addition, the correlations between ion–water stretching motion and other cluster vibrational coordinates are discussed. The results indicate that the intermolecular nuclear quantum effects on the cluster structures are strongly related to the cooperation of the water–water hydrogen bond interactions.

  17. Adsorption and solvation of ethanol at the water liquid-vapor interface: a molecular dynamics study

    Science.gov (United States)

    Wilson, M. A.; Pohorille, A.

    1997-01-01

    The free energy profiles of methanol and ethanol at the water liquid-vapor interface at 310K were calculated using molecular dynamics computer simulations. Both alcohols exhibit a pronounced free energy minimum at the interface and, therefore, have positive adsorption at this interface. The surface excess was computed from the Gibbs adsorption isotherm and was found to be in good agreement with experimental results. Neither compound exhibits a free energy barrier between the bulk and the surface adsorbed state. Scattering calculations of ethanol molecules from a gas phase thermal distribution indicate that the mass accommodation coefficient is 0.98, and the molecules become thermalized within 10 ps of striking the interface. It was determined that the formation of the solvation structure around the ethanol molecule at the interface is not the rate-determining step in its uptake into water droplets. The motion of an ethanol molecule in a water lamella was followed for 30 ns. The time evolution of the probability distribution of finding an ethanol molecule that was initially located at the interface is very well described by the diffusion equation on the free energy surface.

  18. Sulfur dioxide in water: structure and dynamics studied by an ab initio quantum mechanical charge field molecular dynamics simulation.

    Science.gov (United States)

    Moin, Syed Tarique; Lim, Len Herald V; Hofer, Thomas S; Randolf, Bernhard R; Rode, Bernd M

    2011-04-18

    An ab initio Quantum Mechanical Charge Field Molecular Dynamics Simulation (QMCF MD) was performed to investigate structure and dynamics behavior of hydrated sulfur dioxide (SO(2)) at the Hartree-Fock level of theory employing Dunning DZP basis sets for solute and solvent molecules. The intramolecular structural characteristics of SO(2), such as S═O bond lengths and O═S═O bond angle, are in good agreement with the data available from a number of different experiments. The structural features of the hydrated SO(2) were primarily evaluated in the form of S-O(wat) and O(SO(2))-H(wat) radial distribution functions (RDFs) which gave mean distances of 2.9 and 2.2 Å, respectively. The dynamical behavior characterizes the solute molecule to have structure making properties in aqueous solution or water aerosols, where the hydrated SO(2) can easily get oxidized to form a number of sulfur(VI) species, which are believed to play an important role in the atmospheric processes.

  19. Interactions of anesthetics with the water-hexane interface. A molecular dynamics study

    Science.gov (United States)

    Chipot, C.; Wilson, M. A.; Pohorille, A.

    1997-01-01

    The free energy profiles characterizing the transfer of nine solutes across the liquid-vapor interfaces of water and hexane and across the water-hexane interface were calculated from molecular dynamics simulations. Among the solutes were n-butane and three of its halogenated derivatives, as well as three halogenated cyclobutanes. The two remaining molecules, dichlorodifluoromethane and 1,2-dichloroperfluoroethane, belong to series of halo-substituted methanes and ethanes, described in previous studies (J. Chem. Phys. 1996, 104, 3760; Chem. Phys. 1996, 204, 337). Each series of molecules contains structurally similar compounds that differ greatly in anesthetic potency. The accuracy of the simulations was tested by comparing the calculated and the experimental free energies of solvation of all nine compounds in water and in hexane. In addition. the calculated and the measured surface excess concentrations of n-butane at the water liquid-vapor interface were compared. In all cases, good agreement with experimental results was found. At the water-hexane interface, the free energy profiles for polar molecules exhibited significant interfacial minima, whereas the profiles for nonpolar molecules did not. The existence of these minima was interpreted in terms of a balance between the free energy contribution arising from solute-solvent interactions and the work to form a cavity that accommodates the solute. These two contributions change monotonically, but oppositely, across the interface. The interfacial solubilities of the solutes, obtained from the free energy profiles, correlate very well with their anesthetic potencies. This is the case even when the Meyer-Overton hypothesis, which predicts a correlation between anesthetic potency and solubility in oil, fails.

  20. Structure and Dynamics of the Instantaneous Water/Vapor Interface Revisited by Path-Integral and Ab-Initio Molecular Dynamics Simulations

    CERN Document Server

    Kessler, Jan; Spura, Thomas; Karhan, Kristof; Partovi-Azar, Pouya; Hassanali, Ali A; Kühne, Thomas D

    2015-01-01

    The structure and dynamics of the water/vapor interface is revisited by means of path-integral and second-generation Car-Parrinello ab-initio molecular dynamics simulations in conjunction with an instantaneous surface definition [A. P. Willard and D. Chandler, J. Phys. Chem. B 114, 1954 (2010)]. In agreement with previous studies, we find that one of the OH bonds of the water molecules in the topmost layer is pointing out of the water into the vapor phase, while the orientation of the underlying layer is reversed. Therebetween, an additional water layer is detected, where the molecules are aligned parallel to the instantaneous water surface.

  1. Vibrational energy transfer between carbon nanotubes and liquid water: a molecular dynamics study.

    Science.gov (United States)

    Nelson, Tammie R; Chaban, Vitaly V; Kalugin, Oleg N; Prezhdo, Oleg V

    2010-04-08

    The rates and magnitudes of vibrational energy transfer between single-wall carbon nanotubes (CNTs) and water are investigated by classical molecular dynamics. The interactions between the CNT and solvent confined inside of the tube, the CNT and solvent surrounding the tube, as well as the solvent inside and outside of the tube are considered for the (11,11), (15,15), and (19,19) armchair CNTs. The vibrational energy transfer exhibits two time scales, subpicosecond and picosecond, of roughly equal importance. Solvent molecules confined within CNTs are more strongly coupled to the tubes than the outside molecules. The energy exchange is facilitated by slow collective motions, including CNT radial breathing modes (RBM). The transfer rate between CNTs and the inside solvent shows strong dependence on the CNT diameter. In smaller tubes, the transfer is faster and the solvent coupling to RBMs is stronger. The magnitude of the CNT-outside solvent interaction scales with the CNT surface area, while that of the CNT-inside solvent exhibits scaling that is intermediate between the CNT volume and surface. The Coulomb interaction between the solvent molecules inside and outside of the CNTs is much weaker than the CNT-solvent interactions. The results indicate that the excitation energy supplied to CNTs in chemical and biological applications is rapidly deposited to the active molecular agents and should remain localized sufficiently long in order to perform the desired function.

  2. Effect of nanostructure on rapid boiling of water on a hot copper plate: a molecular dynamics study

    Science.gov (United States)

    Fu, Ting; Mao, Yijin; Tang, Yong; Zhang, Yuwen; Yuan, Wei

    2016-08-01

    Molecular dynamic simulations are performed to study the effects of nanostructure on rapid boiling of water that is suddenly heated by a hot copper plate. The results show that the nanostructure has significant effects on energy transfer from solid copper plate to liquid water and phase change process from liquid water to vapor. The liquid water on the solid surface rapidly boil after contacting with an extremely hot copper plate and consequently a cluster of liquid water moves upward during phase change. The temperature of the water film when it separates from solid surface and its final temperature when the system is at equilibrium strongly depend on the size of the nanostructure. These temperatures increase with increasing size of nanostructure. Furthermore, a non-vaporized molecular layer is formed on the surface of the copper plate even continuous heat flux is passing into water domain through the plate.

  3. Void-induced dissolution in molecular dynamics simulations of NaCl and water.

    Science.gov (United States)

    Bahadur, Ranjit; Russell, Lynn M; Alavi, Saman; Martin, Scot T; Buseck, Peter R

    2006-04-21

    To gain a better understanding of the interaction of water and NaCl at the surface during dissolution, we have used molecular dynamics to simulate the interface with two equal-sized slabs of solid NaCl and liquid water in contact. The introduction of voids in the bulk of the salt, as well as steps or pits on the surface of the NaCl slab results in a qualitative change of system structure, as defined by radial distribution functions (RDFs). As an example, the characteristic Na-Na RDF for the system changes from regularly spaced narrow peaks (corresponding to an ordered crystalline structure), to a broad primary and smaller secondary peak (corresponding to a disordered structure). The change is observed at computationally short time scales of 100 ps, in contrast with a much longer time scale of 1 mus expected for complete mixing in the absence of defects. The void fraction (which combines both bulk and surface defects) required to trigger dissolution varies between 15%-20% at 300 K and 1 atm, and has distinct characteristics for the physical breakdown of the crystal lattice. The void fraction required decreases with temperature. Sensitivity studies show a strong dependence of the critical void fraction on the quantity and distribution of voids on the surface, with systems containing a balanced number of surface defects and a rough surface showing a maximum tendency to dissolve. There is a moderate dependence on temperature, with a 5% decrease in required void fraction with a 100 K increase in temperature, and a weak dependence on water potential model used, with the SPC, SPC/E, TIP4P, and RPOL models giving qualitatively identical results. The results were insensitive to the total quantity of water available for dissolution and the duration of the simulation.

  4. Void-induced dissolution in molecular dynamics simulations of NaCl and water

    Science.gov (United States)

    Bahadur, Ranjit; Russell, Lynn M.; Alavi, Saman; Martin, Scot T.; Buseck, Peter R.

    2006-04-01

    To gain a better understanding of the interaction of water and NaCl at the surface during dissolution, we have used molecular dynamics to simulate the interface with two equal-sized slabs of solid NaCl and liquid water in contact. The introduction of voids in the bulk of the salt, as well as steps or pits on the surface of the NaCl slab results in a qualitative change of system structure, as defined by radial distribution functions (RDFs). As an example, the characteristic Na-Na RDF for the system changes from regularly spaced narrow peaks (corresponding to an ordered crystalline structure), to a broad primary and smaller secondary peak (corresponding to a disordered structure). The change is observed at computationally short time scales of 100ps, in contrast with a much longer time scale of 1μs expected for complete mixing in the absence of defects. The void fraction (which combines both bulk and surface defects) required to trigger dissolution varies between 15%-20% at 300K and 1atm, and has distinct characteristics for the physical breakdown of the crystal lattice. The void fraction required decreases with temperature. Sensitivity studies show a strong dependence of the critical void fraction on the quantity and distribution of voids on the surface, with systems containing a balanced number of surface defects and a rough surface showing a maximum tendency to dissolve. There is a moderate dependence on temperature, with a 5% decrease in required void fraction with a 100K increase in temperature, and a weak dependance on water potential model used, with the SPC, SPC/E, TIP4P, and RPOL models giving qualitatively identical results. The results were insensitive to the total quantity of water available for dissolution and the duration of the simulation.

  5. Molecular dynamics of phenol at the liquid-vapor interface of water

    Science.gov (United States)

    Pohorille, Andrew; Benjamin, Ilan

    1991-01-01

    Results of molecular dynamics calculations on phenol at the water liquid-vapor interface are presented. The density profile of the center of mass of phenol exhibits a maximum 1 A from the Gibbs surface toward the vapor phase, indicating that the molecule is surface-active. Changes in the profile caused by the interface extend 6 A from the Gibbs surface into the liquid, significantly more than change in the density profile of water. The most probable orientation of the solute at the surface is such that its symmetry axis is perpendicular to the interface with the OH substituent pointing toward the liquid. An additional simulation with benzene shows that this molecule at the surface most often adopts orientations parallel to the interface. Deeper in the liquid all the solutes are preferentially ordered perpendicular to the surface. In the interfacial region the orientational preferences of the solute are primarily determined by cavity formation needed to accommodate the hydrophobic portion of the dissolved molecule.

  6. Water transport in bentonite: evaluation by molecular dynamics, homogenization analysis and similitude law

    Energy Technology Data Exchange (ETDEWEB)

    Yasuaki, Ichikawa; Somehai, Prayongphan [Nagoya Univ., Dpt. of Environmental Engineering and Architecture, Chikusa, Nagoya (Japan); Kazumi, Kitayama [NUMO, Minato, Tokyo (Japan); Katsuyuki, Kawamura [Tokyo Institute of Technology, Tokyo (Japan)

    2005-07-01

    The major scenario of transport of radioactive nuclides is due to groundwater flow in most HLW projects. The phenomena of water flow and diffusion of chemical species in a bentonite buffer and surrounding rock mass have been treated mainly based on the classical porous media theories under the Darcy law and Fick law. The classical theories involve the following difficulties: 1) True velocity field is hard to be identified, especially in microscale sense. Note that it essentially affects the transport of chemical species. 2) The classical theories are not applicable to the problems in which experimental data are not available. Thus, the very long time behavior cannot be proven. We commonly recognize that the water flow in bentonite and mud-stone is strongly retarded. It is highly doubtful whether the above classical theories are applicable for such very low permeable materials. In this work we first show that the velocity and diffusion fields in pure smectite bentonite can be calculated by a coupled molecular dynamics (MD) simulation and the homogenization analysis (HA). The true velocity field can be calculated by applying HA to the Navier-Stokes equation, and the local distribution of viscosity used in this HA is obtained by MD. The diffusion field is also calculated under the same procedure of MD/HA by using the local diffusion equation with diffusivity calculated by MD. (authors)

  7. Hematite(001)-liquid water interface from hybrid density functional-based molecular dynamics

    Science.gov (United States)

    Falk von Rudorff, Guido; Jakobsen, Rasmus; Rosso, Kevin M.; Blumberger, Jochen

    2016-10-01

    The atom-scale characterisation of interfaces between transition metal oxides and liquid water is fundamental to our mechanistic understanding of diverse phenomena ranging from crystal growth to biogeochemical transformations to solar fuel production. Here we report on the results of large-scale hybrid density functional theory-based molecular dynamics simulations for the hematite(001)-liquid water interface. A specific focus is placed on understanding how different terminations of the same surface influence surface solvation. We find that the two dominant terminations for the hematite(001) surface exhibit strong differences both in terms of the active species formed on the surface and the strength of surface solvation. According to present simulations, we find that charged oxyanions (-O-) and doubly protonated oxygens (-OH2+ ) can be formed on the iron terminated layer via autoionization of neutral -OH groups. No such charged species are found for the oxygen terminated surface. In addition, the missing iron sublayer in the iron terminated surface strongly influences the solvation structure, which becomes less well ordered in the vicinity of the interface. These pronounced differences are likely to affect the reactivity of the two surface terminations, and in particular the energetics of excess charge carriers at the surface.

  8. Molecular dynamics simulations of wetting behavior of water droplets on polytetrafluorethylene surfaces.

    Science.gov (United States)

    Chen, Shuai; Wang, Jiadao; Ma, Tianbao; Chen, Darong

    2014-03-21

    Molecular dynamics simulations are performed to simulate the wetting behavior of nanosized water droplets on flat and pillar polytetrafluorethylene surfaces. The results show that the cutoff of the Lennard-Jones (LJ) potential has a large effect on the simulated value of the contact angle and some suggestions are given on how to choose an appropriate cutoff. On flat surfaces, the contact angle is independent of the size of the water droplet, which was determined by the energy parameters of the LJ potential. Furthermore, on pillar surfaces, two different equilibrium states are present: wetted contact and cross contact. For the wetted contact state, the contact angle increases with increasing droplet size and pillar size within a certain range. However, for the cross contact state, the contact angle and droplet size are uncorrelated, which results from the layering and structuring of molecules after their penetration into the hollows between pillars. However, additional simulations show that the final state depends on the initial geometry and the cross contact state is a metastable wetting state.

  9. Molecular dynamics of phenol at the liquid-vapor interface of water

    Science.gov (United States)

    Pohorille, Andrew; Benjamin, Ilan

    1991-01-01

    Results of molecular dynamics calculations on phenol at the water liquid-vapor interface are presented. The density profile of the center of mass of phenol exhibits a maximum 1 A from the Gibbs surface toward the vapor phase, indicating that the molecule is surface-active. Changes in the profile caused by the interface extend 6 A from the Gibbs surface into the liquid, significantly more than change in the density profile of water. The most probable orientation of the solute at the surface is such that its symmetry axis is perpendicular to the interface with the OH substituent pointing toward the liquid. An additional simulation with benzene shows that this molecule at the surface most often adopts orientations parallel to the interface. Deeper in the liquid all the solutes are preferentially ordered perpendicular to the surface. In the interfacial region the orientational preferences of the solute are primarily determined by cavity formation needed to accommodate the hydrophobic portion of the dissolved molecule.

  10. A hydrated ion model of [UO2] 2 + in water: Structure, dynamics, and spectroscopy from classical molecular dynamics

    Science.gov (United States)

    Pérez-Conesa, Sergio; Torrico, Francisco; Martínez, José M.; Pappalardo, Rafael R.; Sánchez Marcos, Enrique

    2016-12-01

    A new ab initio interaction potential based on the hydrated ion concept has been developed to obtain the structure, energetics, and dynamics of the hydration of uranyl in aqueous solution. It is the first force field that explicitly parameterizes the interaction of the uranyl hydrate with bulk water molecules to accurately define the second-shell behavior. The [UO2(H2O)5 ] 2 + presents a first hydration shell U-O average distance of 2.46 Å and a second hydration shell peak at 4.61 Å corresponding to 22 molecules using a coordination number definition based on a multisite solute cavity. The second shell solvent molecules have longer mean residence times than those corresponding to the divalent monatomic cations. The axial regions are relatively de-populated, lacking direct hydrogen bonding to apical oxygens. Angle-solved radial distribution functions as well as the spatial distribution functions show a strong anisotropy in the ion hydration. The [UO2(H2O)5 ] 2 + solvent structure may be regarded as a combination of a conventional second hydration shell in the equatorial and bridge regions, and a clathrate-like low density region in the axial region. Translational diffusion coefficient, hydration enthalpy, power spectra of the main vibrational modes, and the EXAFS spectrum simulated from molecular dynamics trajectories agree fairly well with the experiment.

  11. Piezoluminescence at the air-water interface through dynamic molecular recognition driven by lateral pressure application.

    Science.gov (United States)

    Ariga, Katsuhiko; Nakanishi, Takashi; Terasaka, Yukiko; Tsuji, Hiromitsu; Sakai, Daisuke; Kikuchi, Jun-ichi

    2005-02-01

    The steroid cyclophanes with a cyclic core consisting of a 1,6,20,25-tetraaza[6.1.6.1]paracyclophane connected to four steroid moieties (cholic acid or cholanic acid) through a flexible l-lysine spacer were spread on water as Langmuir monolayers. The pi-A isotherm of the cholic-type steroid cyclophane includes a transition to the condensed phase with a limiting area of approximately 2 nm(2). This value is close to the cross-sectional area of the steroid cyclophane with a standing-up conformation of the cholic acid moieties, strongly suggesting that the cavity converts from a two-dimensional cavity to a three-dimensional cavity upon compressing the monolayer. Surface-reflective fluorescence spectroscopy of the monolayer using an aqueous fluorescent probe (6-(p-toluidino)naphthalene-2-sulfonate (TNS)) showed an abrupt increase in the TNS fluorescence intensity at a molecular area of 2 nm(2). Efficient binding of the guest probe would occur upon the completion of the three-dimensional cavity. Repeated compression and expansion induces periodic changes in the fluorescence intensity. This indicates a piezoluminescence effect through the catch and release of the TNS guest upon dynamic cavity formation. Analyses of the binding behavior of TNS to the steroid cyclophane resulted in binding constants in the range of approximately (5-9) x 10(4) M(-1) which are similar to that observed in lipid bilayer media (K = 5.1 x 10(4) M(-1)). The fluorescence intensity within the condensed phase was significantly increased with increasing pressure, suggesting that suppression of the molecular motion of the bound TNS may retard the nonemission process. Similar monolayer experiments were carried out with the monolayer of the cholanic-type steroid cyclophane that cannot form an open conformation on water. Both the phase transition in the pi-A isotherm and the change in the fluorescence intensity were negligible, confirming that the dynamic characteristic of the cavity is indispensable for

  12. Homogeneous SPC/E water nucleation in large molecular dynamics simulations

    CERN Document Server

    Angelil, R; Tanaka, K; Tanaka, H

    2015-01-01

    We perform direct large molecular dynamics simulations of homogeneous SPC/E water nucleation, using up to $\\sim 4\\cdot 10^6$ molecules. Our large system sizes allow us to measure extremely low and accurate nucleation rates, down to $\\sim 10^{19}\\,\\textrm{cm}^{-3}\\textrm{s}^{-1}$, helping close the gap between experimentally measured rates $\\sim 10^{17}\\,\\textrm{cm}^{-3}\\textrm{s}^{-1}$. We are also able to precisely measure size distributions, sticking efficiencies, cluster temperatures, and cluster internal densities. We introduce a new functional form to implement the Yasuoka-Matsumoto nucleation rate measurement technique (threshold method). Comparison to nucleation models shows that classical nucleation theory over-estimates nucleation rates by a few orders of magnitude. The semi-phenomenological nucleation model does better, under-predicting rates by at worst, a factor of 24. Unlike what has been observed in Lennard-Jones simulations, post-critical clusters have temperatures consistent with the run avera...

  13. Homogeneous SPC/E water nucleation in large molecular dynamics simulations.

    Science.gov (United States)

    Angélil, Raymond; Diemand, Jürg; Tanaka, Kyoko K; Tanaka, Hidekazu

    2015-08-14

    We perform direct large molecular dynamics simulations of homogeneous SPC/E water nucleation, using up to ∼ 4 ⋅ 10(6) molecules. Our large system sizes allow us to measure extremely low and accurate nucleation rates, down to ∼ 10(19) cm(-3) s(-1), helping close the gap between experimentally measured rates ∼ 10(17) cm(-3) s(-1). We are also able to precisely measure size distributions, sticking efficiencies, cluster temperatures, and cluster internal densities. We introduce a new functional form to implement the Yasuoka-Matsumoto nucleation rate measurement technique (threshold method). Comparison to nucleation models shows that classical nucleation theory over-estimates nucleation rates by a few orders of magnitude. The semi-phenomenological nucleation model does better, under-predicting rates by at worst a factor of 24. Unlike what has been observed in Lennard-Jones simulations, post-critical clusters have temperatures consistent with the run average temperature. Also, we observe that post-critical clusters have densities very slightly higher, ∼ 5%, than bulk liquid. We re-calibrate a Hale-type J vs. S scaling relation using both experimental and simulation data, finding remarkable consistency in over 30 orders of magnitude in the nucleation rate range and 180 K in the temperature range.

  14. TIME-DEPENDENT PROPERTIES OF LIQUID WATER: A COMPARISON OF CAR-PARRINELLO AND BORN-OPPENHIEMER MOLECULAR DYNAMICS SIMULATIONS

    Energy Technology Data Exchange (ETDEWEB)

    Kuo, I W; Mundy, C; McGrath, M; Siepmann, J I

    2005-12-29

    A series of 30 ps first principles molecular dynamics simulations in the microcanonical ensemble were carried out to investigate transport and vibrational properties of liquid water. To allow for sufficient sampling, the thermodynamic constraints were set to an elevated temperature of around 423 K and a density of 0.71 g/cm{sup 3} corresponding to the saturated liquid density for the Becke-Lee-Yang-Parr (BLYP) representation of water. Four simulations using the Car-Parrinello molecular dynamics (CPMD) technique with varying values of the fictitious electronic mass ({mu}) and two simulations using the Born-Oppenheimer molecular dynamics (BOMD) technique are analyzed to yield structural and dynamical information. At the selected state point, the simulations are found to exhibit non-glassy dynamics and yield consistent results for the liquid structure and the self-diffusion coefficient, although the statistical uncertainties in the latter quantity are quite large. Consequently, it can be said that the CPMD and BOMD methods produce equivalent results for these properties on the time scales reported here. However, it was found that the choice of {mu} affects the frequency spectrum of the intramolecular modes, shifting them slightly to regions of lower frequency. Using a value of {mu} = 400 a.u. results in a significant drift in the electronic kinetic energy of the system over the course of 30 ps and a downward drift in the ionic temperature. Therefore, for long trajectories at elevated temperatures, lower values of this parameter are recommended for CPMD simulations of water.

  15. 2D IR spectra of cyanide in water investigated by molecular dynamics simulations

    Science.gov (United States)

    Lee, Myung Won; Carr, Joshua K.; Göllner, Michael; Hamm, Peter; Meuwly, Markus

    2013-01-01

    Using classical molecular dynamics simulations, the 2D infrared (IR) spectroscopy of CN− solvated in D2O is investigated. Depending on the force field parametrizations, most of which are based on multipolar interactions for the CN− molecule, the frequency-frequency correlation function and observables computed from it differ. Most notably, models based on multipoles for CN− and TIP3P for water yield quantitatively correct results when compared with experiments. Furthermore, the recent finding that T 1 times are sensitive to the van der Waals ranges on the CN− is confirmed in the present study. For the linear IR spectrum, the best model reproduces the full widths at half maximum almost quantitatively (13.0 cm−1 vs. 14.9 cm−1) if the rotational contribution to the linewidth is included. Without the rotational contribution, the lines are too narrow by about a factor of two, which agrees with Raman and IR experiments. The computed and experimental tilt angles (or nodal slopes) α as a function of the 2D IR waiting time compare favorably with the measured ones and the frequency fluctuation correlation function is invariably found to contain three time scales: a sub-ps, 1 ps, and one on the 10-ps time scale. These time scales are discussed in terms of the structural dynamics of the surrounding solvent and it is found that the longest time scale (≈10 ps) most likely corresponds to solvent exchange between the first and second solvation shell, in agreement with interpretations from nuclear magnetic resonance measurements.

  16. Molecular dynamics study of nitrobenzene and 2-nitrophenyloctyl ether saturated with water

    OpenAIRE

    Jorge, Miguel; Gulaboski, Rubin; Pereira, Carlos M.; Cordeiro, M. Natália D. S.

    2006-01-01

    In this paper, results obtained from molecular dynamics (MD) simulations on the watersaturated organic liquids nitrobenzene (NB) and 2-nitrophenyloctyl ether (NPOE) are presented. Both solvents are extremely important in many areas of chemistry, and they are seen as the most promising successors of n-octanol for ion transfer studies at the liquid–liquid interface. Thermodynamic (mass density, enthalpy of vaporization), structural (radial distribution functions) and dynamic (dif...

  17. Water droplet excess free energy determined by cluster mitosis using guided molecular dynamics

    Science.gov (United States)

    Lau, Gabriel V.; Hunt, Patricia A.; Müller, Erich A.; Jackson, George; Ford, Ian J.

    2015-12-01

    Atmospheric aerosols play a vital role in affecting climate by influencing the properties and lifetimes of clouds and precipitation. Understanding the underlying microscopic mechanisms involved in the nucleation of aerosol droplets from the vapour phase is therefore of great interest. One key thermodynamic quantity in nucleation is the excess free energy of cluster formation relative to that of the saturated vapour. In our current study, the excess free energy is extracted for clusters of pure water modelled with the TIP4P/2005 intermolecular potential using a method based on nonequilibrium molecular dynamics and the Jarzynski relation. The change in free energy associated with the "mitosis" or division of a cluster of N water molecules into two N/2 sub-clusters is evaluated. This methodology is an extension of the disassembly procedure used recently to calculate the excess free energy of argon clusters [H. Y. Tang and I. J. Ford, Phys. Rev. E 91, 023308 (2015)]. Our findings are compared to the corresponding excess free energies obtained from classical nucleation theory (CNT) as well as internally consistent classical theory (ICCT). The values of the excess free energy that we obtain with the mitosis method are consistent with CNT for large cluster sizes but for the smallest clusters, the results tend towards ICCT; for intermediate sized clusters, we obtain values between the ICCT and CNT predictions. Furthermore, the curvature-dependent surface tension which can be obtained by regarding the clusters as spherical droplets of bulk density is found to be a monotonically increasing function of cluster size for the studied range. The data are compared to other values reported in the literature, agreeing qualitatively with some but disagreeing with the values determined by Joswiak et al. [J. Phys. Chem. Lett. 4, 4267 (2013)] using a biased mitosis approach; an assessment of the differences is the main motivation for our current study.

  18. Water droplet excess free energy determined by cluster mitosis using guided molecular dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Lau, Gabriel V.; Müller, Erich A.; Jackson, George [Department of Chemical Engineering, Imperial College London, South Kensington Campus, London SW7 2AZ (United Kingdom); Hunt, Patricia A. [Department of Chemistry, Imperial College London, South Kensington Campus, London SW7 2AZ (United Kingdom); Ford, Ian J. [Department of Physics and Astronomy and London Centre for Nanotechnology, University College London, Gower Street, London WC1E 6BT (United Kingdom)

    2015-12-28

    Atmospheric aerosols play a vital role in affecting climate by influencing the properties and lifetimes of clouds and precipitation. Understanding the underlying microscopic mechanisms involved in the nucleation of aerosol droplets from the vapour phase is therefore of great interest. One key thermodynamic quantity in nucleation is the excess free energy of cluster formation relative to that of the saturated vapour. In our current study, the excess free energy is extracted for clusters of pure water modelled with the TIP4P/2005 intermolecular potential using a method based on nonequilibrium molecular dynamics and the Jarzynski relation. The change in free energy associated with the “mitosis” or division of a cluster of N water molecules into two N/2 sub-clusters is evaluated. This methodology is an extension of the disassembly procedure used recently to calculate the excess free energy of argon clusters [H. Y. Tang and I. J. Ford, Phys. Rev. E 91, 023308 (2015)]. Our findings are compared to the corresponding excess free energies obtained from classical nucleation theory (CNT) as well as internally consistent classical theory (ICCT). The values of the excess free energy that we obtain with the mitosis method are consistent with CNT for large cluster sizes but for the smallest clusters, the results tend towards ICCT; for intermediate sized clusters, we obtain values between the ICCT and CNT predictions. Furthermore, the curvature-dependent surface tension which can be obtained by regarding the clusters as spherical droplets of bulk density is found to be a monotonically increasing function of cluster size for the studied range. The data are compared to other values reported in the literature, agreeing qualitatively with some but disagreeing with the values determined by Joswiak et al. [J. Phys. Chem. Lett. 4, 4267 (2013)] using a biased mitosis approach; an assessment of the differences is the main motivation for our current study.

  19. Water droplet excess free energy determined by cluster mitosis using guided molecular dynamics.

    Science.gov (United States)

    Lau, Gabriel V; Hunt, Patricia A; Müller, Erich A; Jackson, George; Ford, Ian J

    2015-12-28

    Atmospheric aerosols play a vital role in affecting climate by influencing the properties and lifetimes of clouds and precipitation. Understanding the underlying microscopic mechanisms involved in the nucleation of aerosol droplets from the vapour phase is therefore of great interest. One key thermodynamic quantity in nucleation is the excess free energy of cluster formation relative to that of the saturated vapour. In our current study, the excess free energy is extracted for clusters of pure water modelled with the TIP4P/2005 intermolecular potential using a method based on nonequilibrium molecular dynamics and the Jarzynski relation. The change in free energy associated with the "mitosis" or division of a cluster of N water molecules into two N/2 sub-clusters is evaluated. This methodology is an extension of the disassembly procedure used recently to calculate the excess free energy of argon clusters [H. Y. Tang and I. J. Ford, Phys. Rev. E 91, 023308 (2015)]. Our findings are compared to the corresponding excess free energies obtained from classical nucleation theory (CNT) as well as internally consistent classical theory (ICCT). The values of the excess free energy that we obtain with the mitosis method are consistent with CNT for large cluster sizes but for the smallest clusters, the results tend towards ICCT; for intermediate sized clusters, we obtain values between the ICCT and CNT predictions. Furthermore, the curvature-dependent surface tension which can be obtained by regarding the clusters as spherical droplets of bulk density is found to be a monotonically increasing function of cluster size for the studied range. The data are compared to other values reported in the literature, agreeing qualitatively with some but disagreeing with the values determined by Joswiak et al. [J. Phys. Chem. Lett. 4, 4267 (2013)] using a biased mitosis approach; an assessment of the differences is the main motivation for our current study.

  20. Refinements of water parameters for molecular dynamics: Simulations of adsorption at the clay mineral/aqueous solution interface

    DEFF Research Database (Denmark)

    Schäfer, L.; Yu, C.; Teppen, B.J.;

    1999-01-01

    In the context of a long-term program involving molecular dynamics simulations of adsorption phenomena at the clay mineral/aqueous solution interface, we are testing the viability of combining a force field that we developed specificially for clays with other, independently derived potential...... parameters for molecular species which are important in clay adsorption. For the current study the importance of variations in the potential parameters of water were investigated and polarization effects on oxygen studied as a function of intermolecular interactions. For this purpose ab initio MP2/6-311GG...... atomic charges were determined for several oligomers of water and for the water dimer at different intermolecular separations. Charge variations of up to ~0.1 electron charge unit on oxygen are found and, together with changes in van der Waals constants, their significance for dynamics simulations...

  1. Composition Dependence of Dynamic Heterogeneity Time- and Length Scales in [Omim][BF4]/Water Binary Mixtures: Molecular Dynamics Simulation Study.

    Science.gov (United States)

    Pal, Tamisra; Biswas, Ranjit

    2015-12-24

    Composition dependence of four-point dynamic susceptibilities, overlap functions, and other dynamic heterogeneity (DH) parameters have been investigated by using all-atom molecular dynamics simulations for aqueous solutions of the ionic liquid (IL), 1-octyl-3-methyl imidazolium tetrafluoroborate ([Omim][BF4]) covering the pure-to-pure range. Upon addition of water in the IL, the DH time scales become faster and the four-point dynamic susceptibility time scale softens. Evidences for jump motions for both water and ions have been found from the simulated single particle displacements that show strong deviation from Gaussian distribution. Estimated dynamic correlation length for water reflects effects of IL, whereas those for ions remain largely insensitive to the mixture composition. Simulated structural aspects and DH time scales provide microscopic explanations to the existing experimental observations from time-resolved fluorescence and Kerr spectroscopic measurements.

  2. Molecular dynamics simulations of water confined between matched pairs of hydrophobic and hydrophilic self-assembled monolayers.

    Energy Technology Data Exchange (ETDEWEB)

    Chandross, Michael Evan; Grest, Gary Stephen; Lane, J. Matthew D.; Lorenz, Christian Douglas (King' s College London, London, UK); Stevens, Mark Jackson

    2008-12-01

    We have conducted a molecular dynamics (MD) simulation study of water confined between methyl-terminated and carboxyl-terminated alkylsilane self-assembled monolayers (SAMs) on amorphous silica substrates. In doing so, we have investigated the dynamic and structural behavior of the water molecules when compressed to loads ranging from 20 to 950 MPa for two different amounts of water (27 and 58 water molecules/nm{sup 2}). Within the studied range of loads, we observe that no water molecules penetrate the hydrophobic region of the carboxyl-terminated SAMs. However, we observe that at loads larger than 150 MPa water molecules penetrate the methyl-terminated SAMs and form hydrogen-bonded chains that connect to the bulk water. The diffusion coefficient of the water molecules decreases as the water film becomes thinner and pressure increases. When compared to bulk diffusion coefficients of water molecules at the various loads, we found that the diffusion coefficients for the systems with 27 water molecules/nm{sup 2} are reduced by a factor of 20 at low loads and by a factor of 40 at high loads, while the diffusion coefficients for the systems with 58 water molecules/nm{sup 2} are reduced by a factor of 25 at all loads.

  3. Molecular dynamics modeling of carbon dioxide, water and natural organic matter in Na-hectorite.

    Science.gov (United States)

    Yazaydin, A Ozgur; Bowers, Geoffrey M; Kirkpatrick, R James

    2015-09-28

    Molecular dynamics (MD) modeling of systems containing a Na-exchanged smectite clay (hectorite) and model natural organic matter (NOM) molecules along with pure H2O, pure CO2, or a mixture of H2O and CO2 provides significant new insight into the molecular scale interactions among silicate surfaces, dissolved cations and organic molecules, H2O and CO2 relevant to geological C-sequestration strategies. The simulations for systems containing H2O show the following results; (1) Na(+) does not bridge between NOM molecules and the clay surface at protonation states comparable to near neutral pH conditions. (2) In systems without CO2 the NOM molecules retain charge balancing cations and drift away from the silicate surface. (3) In systems containing both H2O and CO2, the NOM molecules adopt equilibrium positions at the H2O-CO2 interface with the more hydrophilic structural elements facing the H2O and the more hydrophobic ones facing the CO2. In systems with only CO2, NOM and Na(+) ions are pinned to the clay surface with the hydrophilic structural elements of the NOM pointed toward the clay surface. Dynamically, in systems with only CO2, Na(+) diffusion is nearly eliminated, and in systems with a thin water film on the clay surface diffusion perpendicular the surface is greatly reduced relative to the system with bulk water. Energetically, the results for the systems with only H2O show that hydration of the net charge neutral Na-NOM molecule outweighs the sum of its Coulombic and dispersive interactions with the net charge-neutral Na-clay particle and the interactions of the water molecules with the hydrophobic structural elements of the NOM. The aggregation of NOM molecules in solution appears to be driven not by Na(+) bridging between the molecules but by hydrophobic interactions between them. In contrast, for the systems with only CO2 the interaction between the Na-NOM molecules and the CO2 is outweighed by the interaction of NOM with the clay particle. With both H2O

  4. Dynamics of ethanol and water mixtures observed in a self-adjusting molecularly thin slit pore.

    Science.gov (United States)

    Severin, N; Sokolov, I M; Rabe, J P

    2014-04-01

    The structure of multicomponent fluids in confined geometries is a key to understanding their properties. However, it remains an experimental challenge to gain molecular-scale resolution information on this structure. Here we show that mono- and multilayers of graphene, conforming to heterogeneous monolayers of molecules in a flexible slit pore between a mica surface and the graphene layers, allow for mapping the phase separation of water and ethanol within such a slit pore. Employing scanning force microscopy, we readily distinguish clusters of ethanol and water molecules due their different sizes, and we show that the phase separated water-ethanol structures become coarser under thicker graphenes. Moreover, we obtain a lower bound for the two-dimensional diffusion coefficient of ethanol in water of D ≥ 2 × 10(-14) m(2) s(-1). Thus, the molecularly thin slit pore provides a powerful tool to control and to investigate mixed fluids in self-adjusting nanopores.

  5. Structural Interpretation of the Large Slowdown of Water Dynamics at Stacked Phospholipid Membranes for Decreasing Hydration Level: All-Atom Molecular Dynamics

    Directory of Open Access Journals (Sweden)

    Carles Calero

    2016-04-01

    Full Text Available Hydration water determines the stability and function of phospholipid membranes as well as the interaction of membranes with other molecules. Experiments and simulations have shown that water dynamics slows down dramatically as the hydration decreases, suggesting that the interfacial water that dominates the average dynamics at low hydration is slower than water away from the membrane. Here, based on all-atom molecular dynamics simulations, we provide an interpretation of the slowdown of interfacial water in terms of the structure and dynamics of water–water and water–lipid hydrogen bonds (HBs. We calculate the rotational and translational slowdown of the dynamics of water confined in stacked phospholipid membranes at different levels of hydration, from completely hydrated to poorly hydrated membranes. For all hydrations, we analyze the distribution of HBs and find that water–lipids HBs last longer than water–water HBs and that at low hydration most of the water is in the interior of the membrane. We also show that water–water HBs become more persistent as the hydration is lowered. We attribute this effect (i to HBs between water molecules that form, in turn, persistent HBs with lipids; (ii to the hindering of the H-bonding switching between water molecules due to the lower water density at the interface; and (iii to the higher probability of water–lipid HBs as the hydration decreases. Our interpretation of the large dynamic slowdown in water under dehydration is potentially relevant in understanding membrane biophysics at different hydration levels.

  6. Quantum path-integral molecular dynamics calculations of the dipole-bound state of the water dimer anion

    Science.gov (United States)

    Shiga, Motoyuki; Takayanagi, Toshiyuki

    2003-09-01

    The equilibrium structure of the negatively charged water dimer (H 2O) 2- has been studied using the path-integral molecular dynamics simulation. All the atomic motions as well as the excess electron were treated quantum mechanically, employing a semi-empirical model combining a water-water interatomic potential with an electron-water pseudopotential. It is demonstrated that the molecular structure of (H 2O) 2- is more flexible than that of (H 2O) 2; both the donor switching and donor-acceptor interchange can more effectively occur in (H 2O) 2- than in (H 2O) 2. We conclude that this floppy character is a result of the breakdown of the adiabatic Born-Oppenheimer picture.

  7. Molecular dynamics study of the Cu-water interface in the presence of chlorine

    Energy Technology Data Exchange (ETDEWEB)

    Zhou, Y.; Mazzolo, A.; Halley, J.W. [Univ. of Minnesota, Minneapolis, MN (United States). School of Physics and Astronomy; Price, D.L. [Univ. of Memphis, TN (United States). Dept. of Physics

    1998-05-01

    As part of a program to model and explain the sensitivity of electron transfer reactions at metal interfaces to trace amounts of chloride in aqueous solutions, preliminary results on a direct dynamics model for the adsorption of chloride ion on a copper 100 surface in water are reported. The model predicts the charge state of the chlorine in water and vacuum correctly, but gives a solvation energy which is too large. Possible reasons for this are discussed.

  8. Molecular dynamics simulation of water in and around carbon nanotubes: A coarse-grained description

    Science.gov (United States)

    Pantawane, Sanwardhini; Choudhury, Niharendu

    2016-05-01

    In the present study, we intend to investigate behaviour of water in and around hydrophobic open ended carbon nanotubes (CNTs) using a coarse-grained, core-softened model potential for water. The model potential considered here for water has recently been shown to successfully reproduce dynamic, thermodynamic and structural anomalies of water. The epitome of the study is to understand the incarceration of this coarse-grained water in a single-file carbon nanotube. In order to examine the effect of fluid-water van der Waals interaction on the structure of fluid in and around the nanotube, we have simulated three different CNT-water systems with varying degree of solute-water dispersion interaction. The analyses of the radial one-particle density profiles reveal varying degree of permeation and wetting of the CNT interior depending on the degree of fluid-solute attractive van der Waals interaction. A peak in the radial density profile slightly off the nanotube axis signifies a zigzag chain of water molecule around the CNT axis. The average numbers of water molecules inside the CNT have been shown to increase with the increase in fluid-water attractive dispersion interaction.

  9. Molecular dynamics simulation of water in and around carbon nanotubes: A coarse-grained description

    Energy Technology Data Exchange (ETDEWEB)

    Pantawane, Sanwardhini [Department of Physics, UM-DAE Centre for Excellence in Basic Sciences, University of Mumbai, Kalina Campus, Mumbai 400098 (India); Choudhury, Niharendu, E-mail: nihcho@barc.gov.in [Theoretical Chemistry Section, Bhabha Atomic Research Centre, Mumbai 400 085 (India)

    2016-05-23

    In the present study, we intend to investigate behaviour of water in and around hydrophobic open ended carbon nanotubes (CNTs) using a coarse-grained, core-softened model potential for water. The model potential considered here for water has recently been shown to successfully reproduce dynamic, thermodynamic and structural anomalies of water. The epitome of the study is to understand the incarceration of this coarse-grained water in a single-file carbon nanotube. In order to examine the effect of fluid-water van der Waals interaction on the structure of fluid in and around the nanotube, we have simulated three different CNT-water systems with varying degree of solute-water dispersion interaction. The analyses of the radial one-particle density profiles reveal varying degree of permeation and wetting of the CNT interior depending on the degree of fluid-solute attractive van der Waals interaction. A peak in the radial density profile slightly off the nanotube axis signifies a zigzag chain of water molecule around the CNT axis. The average numbers of water molecules inside the CNT have been shown to increase with the increase in fluid-water attractive dispersion interaction.

  10. Water Orientation at Ceramide/Water Interfaces Studied by Heterodyne-Detected Vibrational Sum Frequency Generation Spectroscopy and Molecular Dynamics Simulation

    KAUST Repository

    Adhikari, Aniruddha

    2016-10-10

    Lipid/water interaction is essential for many biological processes. The water structure at the nonionic lipid interface remains little known, and there is no scope of a priori prediction of water orientation at nonionic interfaces, either. Here, we report our study combining advanced nonlinear spectroscopy and molecular dynamics simulation on the water orientation at the ceramide/water interface. We measured χ spectrum in the OH stretch region of ceramide/isotopically diluted water interface using heterodyne-detected vibrational sum-frequency generation spectroscopy and found that the interfacial water prefers an overall hydrogen-up orientation. Molecular dynamics simulation indicates that this preferred hydrogen-up orientation of water is determined by a delicate balance between hydrogen-up and hydrogen-down orientation induced by lipid-water and intralipid hydrogen bonds. This mechanism also suggests that water orientation at neutral lipid interfaces depends highly on the chemical structure of the lipid headgroup, in contrast to the charged lipid interfaces where the net water orientation is determined solely by the charge of the lipid headgroup.

  11. Accurate path integral molecular dynamics simulation of ab-initio water at near-zero added cost

    Science.gov (United States)

    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.).

  12. Liquid Water through Density-Functional Molecular Dynamics: Plane-Wave vs Atomic-Orbital Basis Sets

    CERN Document Server

    Miceli, Giacomo; Pasquarello, Alfredo

    2016-01-01

    We determine and compare structural, dynamical, and electronic properties of liquid water at near ambient conditions through density-functional molecular dynamics simulations, when using either plane-wave or atomic-orbital basis sets. In both frameworks, the electronic structure and the atomic forces are self-consistently determined within the same theoretical scheme based on a nonlocal density functional accounting for van der Waals interactions. The overall properties of liquid water achieved within the two frameworks are in excellent agreement with each other. Thus, our study supports that implementations with plane-wave or atomic-orbital basis sets yield equivalent results and can be used indiscriminately in study of liquid water or aqueous solutions.

  13. Molecular dynamics simulations of trehalose as a 'dynamic reducer' for solvent water molecules in the hydration shell.

    Science.gov (United States)

    Choi, Youngjin; Cho, Kum Won; Jeong, Karpjoo; Jung, Seunho

    2006-06-12

    Systematic computational work for a series of 13 disaccharides was performed to provide an atomic-level insight of unique biochemical role of the alpha,alpha-(1-->1)-linked glucopyranoside dimer over the other glycosidically linked sugars. Superior osmotic and cryoprotective abilities of trehalose were explained on the basis of conformational and hydration characteristics of the trehalose molecule. Analyses of the hydration number and radial distribution function of solvent water molecules showed that there was very little hydration adjacent to the glycosidic oxygen of trehalose and that the dynamic conformation of trehalose was less flexible than any of the other sugars due to this anisotropic hydration. The remarkable conformational rigidity that allowed trehalose to act as a sugar template was required for stable interactions with hydrogen-bonded water molecules. Trehalose made an average of 2.8 long-lived hydrogen bonds per each MD step, which was much larger than the average of 2.1 for the other sugars. The stable hydrogen-bond network is derived from the formation of long-lived water bridges at the expense of decreasing the dynamics of the water molecules. Evidence for this dynamic reduction of water by trehalose was also established based on each of the lowest translational diffusion coefficients and the lowest intermolecular coulombic energy of the water molecules around trehalose. Overall results indicate that trehalose functions as a 'dynamic reducer' for solvent water molecules based on its anisotropic hydration and conformational rigidity, suggesting that macroscopic solvent properties could be modulated by changes in the type of glycosidic linkages in sugar molecules.

  14. Molecular Dynamics of Equilibrium and Pressure-Driven Transport Properties of Water through LTA-Type Zeolites

    KAUST Repository

    Turgman-Cohen, Salomon

    2013-10-08

    We consider an atomistic model to investigate the flux of water through thin Linde type A (LTA) zeolite membranes with differing surface chemistries. Using molecular dynamics, we have studied the flow of water under hydrostatic pressure through a fully hydrated LTA zeolite film (∼2.5 nm thick) capped with hydrophilic and hydrophobic moieties. Pressure drops in the 50-400 MPa range were applied across the membrane, and the flux of water was monitored for at least 15 ns of simulation time. For hydrophilic membranes, water molecules adsorb at the zeolite surface, creating a highly structured fluid layer. For hydrophobic membranes, a depletion of water molecules occurs near the water/zeolite interface. For both types of membranes, the water structure is independent of the pressure drop established in the system and the flux through the membranes is lower than that observed for the bulk zeolitic material; the latter allows an estimation of surface barrier effects to pressure-driven water transport. Mechanistically, it is observed that (i) bottlenecks form at the windows of the zeolite structure, preventing the free flow of water through the porous membrane, (ii) water molecules do not move through a cage in a single-file fashion but rather exhibit a broad range of residence times and pronounced mixing, and (iii) a periodic buildup of a pressure difference between inlet and outlet cages takes place which leads to the preferential flow of water molecules toward the low-pressure cages. © 2013 American Chemical Society.

  15. Diffusion and reaction pathways of water near fully hydrated TiO2 surfaces from ab initio molecular dynamics

    Science.gov (United States)

    Agosta, Lorenzo; Brandt, Erik G.; Lyubartsev, Alexander P.

    2017-07-01

    Ab initio molecular dynamics simulations are reported for water-embedded TiO2 surfaces to determine the diffusive and reactive behavior at full hydration. A three-domain model is developed for six surfaces [rutile (110), (100), and (001), and anatase (101), (100), and (001)] which describes waters as "hard" (irreversibly bound to the surface), "soft" (with reduced mobility but orientation freedom near the surface), or "bulk." The model explains previous experimental data and provides a detailed picture of water diffusion near TiO2 surfaces. Water reactivity is analyzed with a graph-theoretic approach that reveals a number of reaction pathways on TiO2 which occur at full hydration, in addition to direct water splitting. Hydronium (H3O+) is identified to be a key intermediate state, which facilitates water dissociation by proton hopping between intact and dissociated waters near the surfaces. These discoveries significantly improve the understanding of nanoscale water dynamics and reactivity at TiO2 interfaces under ambient conditions.

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

    Science.gov (United States)

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

    2017-03-22

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

  17. Ab Initio Molecular Dynamics Study on the Interactions between Carboxylate Ions and Metal Ions in Water.

    Science.gov (United States)

    Mehandzhiyski, Aleksandar Y; Riccardi, Enrico; van Erp, Titus S; Trinh, Thuat T; Grimes, Brian A

    2015-08-20

    The interaction between a carboxylate anion (deprotonated propanoic acid) and the divalent Mg(2+), Ca(2+), Sr(2+), Ba(2+) metal ions is studied via ab initio molecular dynamics. The main focus of the study is the selectivity of the carboxylate-metal ion interaction in aqueous solution. The interaction is modeled by explicitly accounting for the solvent molecules on a DFT level. The hydration energies of the metal ions along with their diffusion and mobility coefficients are determined and a trend correlated with their ionic radius is found. Subsequently, a series of 16 constrained molecular dynamics simulations for every ion is performed, and the interaction free energy is obtained from thermodynamic integration of the forces between the metal ion and the carboxylate ion. The results indicate that the magnesium ion interacts most strongly with the carboxylate, followed by calcium, strontium, and barium. Because the interaction free energy is not enough to explain the selectivity of the reaction observed experimentally, more detailed analysis is performed on the simulation trajectories to understand the steric changes in the reaction complex during dissociation. The solvent dynamics appear to play an important role during the dissociation of the complex and also in the observed selectivity behavior of the divalent ions.

  18. Molecular dynamics test of the Brownian description of Na(+) motion in water

    Science.gov (United States)

    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.

  19. Molecular dynamics test of the Brownian description of Na(+) motion in water

    Science.gov (United States)

    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.

  20. Interaction between water molecules and zinc sulfide nanoparticles studied by temperature-programmed desorption and molecular dynamics simulations.

    Science.gov (United States)

    Zhang, Hengzhong; Rustad, James R; Banfield, Jillian F

    2007-06-14

    We have investigated the bonding of water molecules to the surfaces of ZnS nanoparticles (approximately 2-3 nm sphalerite) using temperature-programmed desorption (TPD). The activation energy for water desorption was derived as a function of the surface coverage through kinetic modeling of the experimental TPD curves. The binding energy of water equals the activation energy of desorption if it is assumed that the activation energy for adsorption is nearly zero. Molecular dynamics (MD) simulations of water adsorption on 3 and 5 nm sphalerite nanoparticles provided insights into the adsorption process and water binding at the atomic level. Water binds with the ZnS nanoparticle surface mainly via formation of Zn-O bonds. As compared with bulk ZnS crystals, ZnS nanoparticles can adsorb more water molecules per unit surface area due to the greatly increased curvature, which increases the distance between adjacent adsorbed molecules. Results from both TPD and MD show that the water binding energy increases with decreasing the water surface coverage. We attribute the increase in binding energy with decreasing surface water coverage to the increasing degree of surface under-coordination as removal of water molecules proceeds. MD also suggests that the water binding energy increases with decreasing particle size due to the further distance and hence lower interaction between adsorbed water molecules on highly curved smaller particle surfaces. Results also show that the binding energy, and thus the strength of interaction of water, is highest in isolated nanoparticles, lower in nanoparticle aggregates, and lowest in bulk crystals. Given that water binding is driven by surface energy reduction, we attribute the decreased binding energy for aggregated as compared to isolated particles to the decrease in surface energy that occurs as the result of inter-particle interactions.

  1. Communication: Librational dynamics in water, sI and sII clathrate hydrates, and ice Ih: Molecular-dynamics insights.

    Science.gov (United States)

    Burnham, Christian J; English, Niall J

    2016-02-01

    Equilibrium molecular-dynamics simulations have been performed for liquid water, and on metastable sI and sII polymorphs of empty hydrate lattices, in addition to ice Ih, in order to study the dynamical properties of librational motion (rotation oscillation) depicted by protons in water molecules. In particular, hydrate lattices were found to display prominent "bifurcated" features, or peaks, at circa 70 and 80-95 meV (or ∼560 and 640-760 cm(-1), respectively), also displayed by ice, in essentially quantitative agreement with experimental neutron-scattering data. However, observed differences in dispersion between these librational modes between these two structures (both hydrate polymorphs vis-à-vis ice), owing primarily to density effects, have been decomposed into contributions arising from angular-velocity dynamics about axes in the local molecular frame of water molecules, with in-plane "wagging" and "twisting" rationalising one mode at ∼70 meV, and out-of-plane motion for the higher-frequency band. This was confirmed explicitly by a type of de facto normal-mode analysis, in which only immediate layers of water molecules about the one under consideration were allowed to move. In contrast, liquid water displayed no marked preference for such local in- or out-of-plane modes characterising librational motion, owing to the marked absence of rigid, pentamers or hexamers therein.

  2. Communication: Librational dynamics in water, sI and sII clathrate hydrates, and ice Ih: Molecular-dynamics insights

    Science.gov (United States)

    Burnham, Christian J.; English, Niall J.

    2016-02-01

    Equilibrium molecular-dynamics simulations have been performed for liquid water, and on metastable sI and sII polymorphs of empty hydrate lattices, in addition to ice Ih, in order to study the dynamical properties of librational motion (rotation oscillation) depicted by protons in water molecules. In particular, hydrate lattices were found to display prominent "bifurcated" features, or peaks, at circa 70 and 80-95 meV (or ˜560 and 640-760 cm-1, respectively), also displayed by ice, in essentially quantitative agreement with experimental neutron-scattering data. However, observed differences in dispersion between these librational modes between these two structures (both hydrate polymorphs vis-à-vis ice), owing primarily to density effects, have been decomposed into contributions arising from angular-velocity dynamics about axes in the local molecular frame of water molecules, with in-plane "wagging" and "twisting" rationalising one mode at ˜70 meV, and out-of-plane motion for the higher-frequency band. This was confirmed explicitly by a type of de facto normal-mode analysis, in which only immediate layers of water molecules about the one under consideration were allowed to move. In contrast, liquid water displayed no marked preference for such local in- or out-of-plane modes characterising librational motion, owing to the marked absence of rigid, pentamers or hexamers therein.

  3. Nonequilibrium molecular dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Hoover, W.G. (California Univ., Davis, CA (USA). Dept. of Applied Science Lawrence Livermore National Lab., CA (USA))

    1990-11-01

    The development of nonequilibrium molecular dynamics is described, with emphasis on massively-parallel simulations involving the motion of millions, soon to be billions, of atoms. Corresponding continuum simulations are also discussed. 14 refs., 8 figs.

  4. MOLECULAR DYNAMICS SIMULATIONS OF FILLED AND EMPTY CAGE-LIKE WATER CLUSTERS IN LIQUID WATER AND THEIR SIGNIFICANCE TO GAS HYDRATE FORMATION MECHANISMS

    Institute of Scientific and Technical Information of China (English)

    GUO Guangjun; ZHANG Yigang; ZHAO Yajuan

    2003-01-01

    Molecular dynamics simulations are performed to observe the evolutions of 512 and 51262 cage-like water clusters filled with or without a methane molecule immersed in bulk liquid water at 250 K and 230 K. The lifetimes of these clusters are calculated according to their Lindemann index δ (t) using the criteria of δ≥0.07. For both the filled and empty clusters, we find the dynamics of bulk water determines the lifetimes of cage-like water clusters, and that the lifetime of 512 62 cage-like cluster is the same as that of 512 cage-like cluster. Although the methane molecule indeed makes the filled cage-like cluster more stable than the empty one, the empty cage-like cluster still has chance to be long-lived compared with the filled clusters. These observations support the labile cluster hypothesis on the formation mechanisms of gas hydrates.

  5. A molecular dynamics investigation of the influence of water structure on ion conduction through a carbon nanotube

    Science.gov (United States)

    Liu, L.; Patey, G. N.

    2017-02-01

    Molecular dynamics simulations are employed to investigate pressure-driven water and ion transport through a (9,9) carbon nanotube (CNT). We consider NaCl solutions modeled with both the TIP3P and TIP4P/2005 water models. Concentrations range from 0.25 to 2.8 mol l-1 and temperatures from 260 to 320 K are considered. We discuss the influences on flow rates of continuum hydrodynamic considerations and molecular structural effects. We show that the flow rate of water, sodium, and chloride ions through the CNT is strongly model dependent, consistent with earlier simulations of pure water conduction. To remove the effects of different water flow rates, and clearly expose the influence of other factors on ion flow, we calculate ion transport efficiencies. Ion transport efficiencies are much smaller for TIP4P/2005 solutions than for those using the TIP3P model. Particularly at lower temperatures, the ion transport efficiencies for the TIP4P/2005 model are small, despite the fact that the nanotube conducts water at a significant rate. We trace the origin of small ion transport efficiencies to the presence of ring-like water structures within the CNT. Such structures occur commonly for the TIP4P/2005 model, but less frequently for TIP3P. The water structure acts to reduce ion "solvation" within the CNT, posing an additional barrier to ion entry and transport. Our results demonstrate that increasing the water structure within the CNT by decreasing the temperature strongly inhibits ion conduction, while still permitting significant water transport.

  6. Molecular dynamics simulation of diffusivity

    Institute of Scientific and Technical Information of China (English)

    Juanfang LIU; Danling ZENG; Qin LI; Hong GAO

    2008-01-01

    Equilibrium molecular dynamics simulation was performed on water to calculate its diffusivity by adopting different potential models. The results show that the potential models have great influence on the simulated results. In addition, the diffusivities obtained by the SPCE model conform well to the experimental values.

  7. Molecular dynamics simulations

    OpenAIRE

    Tarmyshov, Konstantin B.

    2007-01-01

    Molecular simulations can provide a detailed picture of a desired chemical, physical, or biological process. It has been developed over last 50 years and is being used now to solve a large variety of problems in many different fields. In particular, quantum calculations are very helpful to study small systems at a high resolution where electronic structure of compounds is accounted for. Molecular dynamics simulations, in turn, are employed to study development of a certain molecular ensemble ...

  8. An insight to conserved water molecular dynamics of catalytic and structural Zn(+2) ions in matrix metalloproteinase 13 of human.

    Science.gov (United States)

    Chakrabarti, Bornali; Bairagya, Hridoy R; Mallik, Payel; Mukhopadhyay, Bishnu P; Bera, Asim K

    2011-02-01

    Matrix Metalloproteinase (MMP)--13 or Collagenase--3 plays a significant role in the formation and remodeling of bone, tumor invasion and causes osteoarthritis. Water molecular dynamic studies of the five (1XUC, 1XUD, 1XUR, 456C, 830C) PDB and solvated structures of MMP-13 in human have been carried out upto 5 ns on assigning the differential charges (+2, +1, +0.5 e) to both the Zinc ions. The MM and MD-studies have revealed the coordination of three water molecules (W(H), W(I) and W(S)) to Zn(c) and one water to Zn(s). The transition of geometry around the Znc from tetrahedral to octahedral via trigonal bipyramidal, and for Zn(s) from tetrahedral to trigonal bipyramidal are seem interesting. Recognition of two zinc ions through water molecular bridging (Zn(c) - W(H) (W(1))...W(2)....W(3)....H(187) Zn(s)) and the stabilization of variable coordination geometries around metal ions may indicate the possible involvement of Zn(c) ...Zn(s) coupled mechanism in the catalytic process. So the hydrophilic topology and stereochemistry of water mediated coupling between Zn-ions may provide some plausible hope towards the design of some bidentate/polydentate bridging ligands or inhibitors for MMP-13.

  9. Molecular dynamics simulation reveals conformational switching of water-mediated uracil-cytosine base-pairs in an RNA duplex.

    Science.gov (United States)

    Schneider, C; Brandl, M; Sühnel, J

    2001-01-26

    A 4 ns molecular dynamics simulation of an RNA duplex (r-GGACUUCGGUCC)(2 )in solution with Na+ and Cl- as counterions was performed. The X-ray structure of this duplex includes two water-mediated uracil-cytosine pairs. In contrast to the other base-pairs in the duplex the water-mediated pairs switch between different conformations. One conformation corresponds to the geometry of the water-mediated UC pairs in the duplex X-ray structure with water acting both as hydrogen-bond donor and acceptor. Another conformation is close to that of a water-mediated UC base-pair found in the X-ray structure of the 23 S rRNA sarcin/ricin domain. In this case the oxygen of the water molecule is linked to two-base donor sites. For a very short time also a direct UC base-pair and a further conformation that is similar to the one found in the RNA duplex structure but exhibits an increased H3(U)...N3(C) distance is observed. Water molecules with unusually long residence times are involved in the water-mediated conformations. These results indicate that the dynamic behaviour of the water-mediated UC base-pairs differs from that of the duplex Watson-Crick and non-canonical guanine-uracil pairs with two or three direct hydrogen bonds. The conformational variability and increased flexibility has to be taken into account when considering these base-pairs as RNA building blocks and as recognition motifs. Copyright 2001 Academic Press.

  10. Self-assembly of single-walled carbon nanotubes into multiwalled carbon nanotubes in water: molecular dynamics simulations.

    Science.gov (United States)

    Zou, Jian; Ji, Baohua; Feng, Xi-Qiao; Gao, Huajian

    2006-03-01

    We report discoveries from a series of molecular dynamics simulations that single-walled carbon nanotubes, with different diameters, lengths, and chiralities, can coaxially self-assemble into multiwalled carbon nanotubes in water via spontaneous insertion of smaller tubes into larger ones. The assembly process is tube-size-dependent, and the driving force is primarily the intertube van der Waals interactions. The simulations also suggest that a multiwalled carbon nanotube may be separated into single-walled carbon nanotubes under appropriate solvent conditions. This study suggests possible bottom-up self-assembly routes for the fabrication of novel nanodevices and systems.

  11. Molecular dynamics simulations of the adsorption of amino acids on the hydroxyapatite {100}-water interface

    Institute of Scientific and Technical Information of China (English)

    Zhi-sen ZHANG; Hai-hua PAN; Rui-kang TANG

    2008-01-01

    The understanding of interfaces and interaction of organic molecules and inorganic materials are the important issues in biomineralization. Experimentally, it has been found that amino acids (AA) can regulate the morphology of hydroxyapatite (HAP) crystals significantly. In this study, molecular dynamics simulation is employed to investigate the detailed adsorption behavior of polar, ionic, and hydrophobic AA on the {100} face of HAP at the atomic level. The results indicate that various AA are adsorbed on the HAP crystal surface mainly by amino and carboxylate groups at the specific sites. Multiple inter-action points are found for polar and ionic AA. The adsorbed AA molecules occupy the Ca and P sites of the HAP surfaces which may inhibit and regulate the HAP growth. The adsorbed amino acid layer can also change the interfacial hydration layer and influence the transporta-tion of ions in and out of HAP, which may be another strategy of biological control in biomineralization.

  12. Effect of Cu2+ Activation on Interfacial Water Structure at the Sphalerite Surface as Studied by Molecular Dynamics Simulation

    Energy Technology Data Exchange (ETDEWEB)

    Jin, Jiaqi; Miller, Jan D.; Dang, Liem X.; Wick, Collin D.

    2015-12-10

    In the first part of this paper, an experimental contact angle study of the fresh and Cu2+ activated sphalerite-ZnS surface as well as the covellite-CuS (001) surface is reported describing the increased hydrophobic character of the surface during Cu2+ activation. In addition to these experimental results, the fresh sphalerite-ZnS (110), copper-zinc sulfide-CuZnS2 (110), villamaninite- CuS2 (100), and covellite-CuS (001) surfaces were examined using Molecular Dynamics Simulation (MDS). Our MDS results on the behavior of interfacial water at the fresh sphalerite-ZnS (110), copper-zinc sulfide-CuZnS2 (110), villamaninite-CuS2 (100), and covellite-CuS (001) surfaces include simulated contact angles, water number density distribution, water dipole orientation, water residence time, and hydrogen-bonding considerations. The copper content at the Cu2+ activated sphalerite surface seems to account for the increased hydrophobicity as revealed by both experimental and MD simulated contact angle measurements. The relatively greater hydrophobic character developed at the Cu2+ activated sphalerite surface and at the copper-zinc sulfide surface has been described by MDS, based on the structure of interfacial water and its dynamic properties. L.X.D. acknowledges funding from the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences, and Biosciences.

  13. Molecular dynamics simulations of the dynamic and energetic properties of alkali and halide ions using water-model-specific ion parameters.

    Science.gov (United States)

    Joung, In Suk; Cheatham, Thomas E

    2009-10-01

    The dynamic and energetic properties of the alkali and halide ions were calculated using molecular dynamics (MD) and free energy simulations with various different water and ion force fields including our recently developed water-model-specific ion parameters. The properties calculated were activity coefficients, diffusion coefficients, residence times of atomic pairs, association constants, and solubility. Through calculation of these properties, we can assess the validity and range of applicability of the simple pair potential models and better understand their limitations. Due to extreme computational demands, the activity coefficients were only calculated for a subset of the models. The results qualitatively agree with experiment. Calculated diffusion coefficients and residence times between cation-anion, water-cation, and water-anion showed differences depending on the choice of water and ion force field used. The calculated solubilities of the alkali-halide salts were generally lower than the true solubility of the salts. However, for both the TIP4P(EW) and SPC/E water-model-specific ion parameters, solubility was reasonably well-reproduced. Finally, the correlations among the various properties led to the following conclusions: (1) The reliability of the ion force fields is significantly affected by the specific choice of water model. (2) Ion-ion interactions are very important to accurately simulate the properties, especially solubility. (3) The SPC/E and TIP4P(EW) water-model-specific ion force fields are preferred for simulation in high salt environments compared to the other ion force fields.

  14. Polymer friction Molecular Dynamics

    DEFF Research Database (Denmark)

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

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

  15. Effect of water on structure and dynamics of [BMIM][PF6] ionic liquid: An all-atom molecular dynamics simulation investigation

    Science.gov (United States)

    Sharma, Anirban; Ghorai, Pradip Kr.

    2016-03-01

    Composition dependent structural and dynamical properties of aqueous hydrophobic 1-butyl-3-methylimidazolium hexafluorophosphate ([BMIM][PF6]) ionic liquid (IL) have been investigated by using all-atom molecular dynamics simulation. We observe that addition of water does not increase significant number of dissociated ions in the solution over the pure state. As a consequence, self-diffusion coefficient of the cation and anion is comparable to each other at all water concentration similar to that is observed for the pure state. Voronoi polyhedra analysis exhibits strong dependence on the local environment of IL concentration. Void and neck distributions in Voronoi tessellation are approximately Gaussian for pure IL but upon subsequent addition of water, we observe deviation from the Gaussian behaviour with an asymmetric broadening with long tail of exponential decay at large void radius, particularly at higher water concentrations. The increase in void space and neck size at higher water concentration facilitates ionic motion, thus, decreasing dynamical heterogeneity and IL reorientation time and increases self-diffusion coefficient significantly.

  16. Hydration properties of lanthanoid(III) carbonate complexes in liquid water determined by polarizable molecular dynamics simulations.

    Science.gov (United States)

    Martelli, Fausto; Jeanvoine, Yannick; Vercouter, Thomas; Beuchat, César; Vuilleumier, Rodolphe; Spezia, Riccardo

    2014-02-28

    In this work we have studied the structure and dynamics of complexes formed by three and four carbonates and a central lanthanoid(III) ion in liquid water by means of polarizable molecular dynamics simulations. With this aim we have developed a force field employing an extrapolation procedure that was previously developed for lanthanoid(III) aqua ions and then we have validated it against DFT-based data. In this way we were able to shed light on properties of the whole series, finding some similarities and differences across the series, and to help in interpreting experiments on those systems. We found that the bi-dentate tri-carbonate complexes are the most stable for all the atoms, but a variation of the number of water molecules in the first ion shell, and the associated exchange dynamics, is observed from lighter to heavier elements. On the other hand, for four-carbonate systems only one water molecule is observed in the first shell, with 10-20% probability, for La(III) and Ce(III), while for the rest of the series it seems impossible for a water molecule to enter the first ion shell in the presence of such an excess of carbonate ligands. Finally, the good performance of our extrapolation procedure, based on ionic radii, makes us confident in extending such approaches to study the structure and dynamics of other systems in solution containing Ln(III) and An(III) ions. This parametrization method results particularly useful since it does not need expensive quantum chemistry calculations for all the atoms in the series.

  17. Molecular dynamics simulations of triflic acid and triflate ion/water mixtures: a proton conducting electrolytic component in fuel cells.

    Science.gov (United States)

    Sunda, Anurag Prakash; Venkatnathan, Arun

    2011-11-30

    Triflic acid is a functional group of perflourosulfonated polymer electrolyte membranes where the sulfonate group is responsible for proton conduction. However, even at extremely low hydration, triflic acid exists as a triflate ion. In this work, we have developed a force-field for triflic acid and triflate ion by deriving force-field parameters using ab initio calculations and incorporated these parameters with the Optimized Potentials for Liquid Simulations - All Atom (OPLS-AA) force-field. We have employed classical molecular dynamics (MD) simulations with the developed force field to characterize structural and dynamical properties of triflic acid (270-450 K) and triflate ion/water mixtures (300 K). The radial distribution functions (RDFs) show the hydrophobic nature of CF(3) group and presence of strong hydrogen bonding in triflic acid and temperature has an insignificant effect. Results from our MD simulations show that the diffusion of triflic acid increases with temperature. The RDFs from triflate ion/water mixtures shows that increasing hydration causes water molecules to orient around the SO(3)(-) group of triflate ions, solvate the hydronium ions, and other water molecules. The diffusion of triflate ions, hydronium ion, and water molecules shows an increase with hydration. At λ = 1, the diffusion of triflate ion is 30 times lower than the diffusion of triflic acid due to the formation of stable triflate ion-hydronium ion complex. With increasing hydration, water molecules break the stability of triflate ion-hydronium ion complex leading to enhanced diffusion. The RDFs and diffusion coefficients of triflate ions, hydronium ions and water molecules resemble qualitatively the previous findings using per-fluorosulfonated membranes.

  18. Coarse-grained molecular dynamics simulations of shear-induced instabilities of lipid bilayer membranes in water

    Science.gov (United States)

    Hanasaki, Itsuo; Walther, Jens H.; Kawano, Satoyuki; Koumoutsakos, Petros

    2010-11-01

    We study shear-induced instabilities of lipid bilayers immersed in water using coarse-grained molecular dynamics simulations. The shear imposed by the flow of the water induces initially microscopic structural changes of the membrane, starting with tilting of the molecules in the direction of the shear. The tilting propagates in the spanwise direction when the shear rate exceeds a critical value and the membrane undergoes a bucklinglike deformation in the direction perpendicular to the shear. The bucklinglike undulation continues until a localized Kelvin-Helmholtz-like instability leads to membrane rupture. We study the different modes of membrane undulation using membranes of different geometries and quantify the relative importance of the bucklinglike bending and the Kelvin-Helmholtz-like instability of the membrane.

  19. Molecular Dynamics Simulations of the Nucleation of Water: Determining the Sticking Probability and Formation Energy of a Cluster

    CERN Document Server

    Tanaka, Kyoko K; Tanaka, Hidekazu

    2014-01-01

    We performed molecular dynamics (MD) simulations of the nucleation of water vapor in order to test nucleation theories. Simulations were performed for a wide range of supersaturation ratios (S = 3-25) and water temperatures (Tw=300-390K). We obtained the nucleation rates and the formation free energies of a subcritical cluster from the cluster size distribution. The classical nucleation theory (CNT) and the modified classical nucleation theory (MCNT) overestimate the nucleation rates in all cases. The semi-phenomenological (SP) model, which corrects the MCNT prediction using the second virial coefficient of a vapor, reproduces the formation free energy of a cluster with the size < 20 to within 10 % and the nucleation rate and cluster size distributions to within one order of magnitude. The sticking probability of the vapor molecules to the clusters was also determined from the growth rates of the clusters. The sticking probability rapidly increases with the supersaturation ratio S, which is similar to the ...

  20. Water exit pathways and proton pumping mechanism in B-type cytochrome c oxidase from molecular dynamics simulations.

    Science.gov (United States)

    Yang, Longhua; Skjevik, Åge A; Han Du, Wen-Ge; Noodleman, Louis; Walker, Ross C; Götz, Andreas W

    2016-09-01

    Cytochrome c oxidase (CcO) is a vital enzyme that catalyzes the reduction of molecular oxygen to water and pumps protons across mitochondrial and bacterial membranes. While proton uptake channels as well as water exit channels have been identified for A-type CcOs, the means by which water and protons exit B-type CcOs remain unclear. In this work, we investigate potential mechanisms for proton transport above the dinuclear center (DNC) in ba3-type CcO of Thermus thermophilus. Using long-time scale, all-atom molecular dynamics (MD) simulations for several relevant protonation states, we identify a potential mechanism for proton transport that involves propionate A of the active site heme a3 and residues Asp372, His376 and Glu126(II), with residue His376 acting as the proton-loading site. The proposed proton transport process involves a rotation of residue His376 and is in line with experimental findings. We also demonstrate how the strength of the salt bridge between residues Arg225 and Asp287 depends on the protonation state and that this salt bridge is unlikely to act as a simple electrostatic gate that prevents proton backflow. We identify two water exit pathways that connect the water pool above the DNC to the outer P-side of the membrane, which can potentially also act as proton exit transport pathways. Importantly, these water exit pathways can be blocked by narrowing the entrance channel between residues Gln151(II) and Arg449/Arg450 or by obstructing the entrance through a conformational change of residue Tyr136, respectively, both of which seem to be affected by protonation of residue His376.

  1. Molecular Dynamics Simulation: The Behavior of Asphaltene in Crude Oil and at the Oil/Water Interface

    KAUST Repository

    Gao, Fengfeng

    2014-12-18

    Carboxyl asphaltene is commonly discussed in the petroleum industry. In most conditions, electroneutral carboxyl asphaltene molecules can be deprotonated to become carboxylate asphaltenes. Both in crude oil and at the oil/water interface, the characteristics of anionic carboxylate asphaltenes are different than those of the carboxyl asphaltenes. In this paper, molecular dynamics (MD) simulations are utilized to study the structural features of different asphaltene molecules, namely, C5 Pe and anionic C5 Pe, at the molecular level. In crude oil, the electroneutral C5 Pe molecules prefer to form a steady face-to-face stacking, while the anionic C5 Pe molecules are inclined to form face-to-face stacking and T-shaped II stacking because of the repulsion of the anionic headgroups. Anionic C5 Pe has a distinct affinity to the oil/water interface during the simulation, while the C5 Pe molecules persist in the crude oil domain. A three-stage model of anionic C5 Pe molecules adsorbed at the oil/water interface is finally developed.

  2. Polymer and Water Dynamics in Poly(vinyl alcohol/Poly(methacrylate Networks. A Molecular Dynamics Simulation and Incoherent Neutron Scattering Investigation

    Directory of Open Access Journals (Sweden)

    Ester Chiessi

    2011-10-01

    Full Text Available Chemically cross-linked polymer networks of poly(vinyl alcohol/poly(methacrylate form monolitic hydrogels and microgels suitable for biomedical applications, such as in situ tissue replacement and drug delivery. In this work, molecular dynamics (MD simulation and incoherent neutron scattering methods are used to study the local polymer dynamics and the polymer induced modification of water properties in poly(vinyl alcohol/poly(methacrylate hydrogels. This information is particularly relevant when the diffusion of metabolites and drugs is a requirement for the polymer microgel functionality. MD simulations of an atomic detailed model of the junction domain at the experimental hydration degree were carried out at 283, 293 and 313 K. The polymer-water interaction, the polymer connectivity and the water dynamics were investigated as a function of temperature. Simulation results are compared with findings of elastic and quasi-elastic incoherent neutron scattering measurements, experimental approaches which sample the same space-time window of MD simulations. This combined analysis shows a supercooled water component and an increase of hydrophilicity and mobility with temperature of these amphiphilic polymer networks.

  3. Analysis of Mesoscopic Structured 2-Propanol/Water Mixtures Using Pressure Perturbation Calorimetry and Molecular Dynamic Simulation.

    Science.gov (United States)

    Bye, Jordan W; Freeman, Colin L; Howard, John D; Herz, Gregor; McGregor, James; Falconer, Robert J

    2017-01-01

    In this paper we demonstrate the application of pressure perturbation calorimetry (PPC) to the characterization of 2-propanol/water mixtures. PPC of different 2-propanol/water mixtures provides two useful measurements: (i) the change in heat (ΔQ); and (ii) the [Formula: see text] value. The results demonstrate that the ΔQ values of the mixtures deviate from that expected for a random mixture, with a maximum at ~20-25 mol% 2-propanol. This coincides with the concentration at which molecular dynamics (MD) simulations show a maximum deviation from random distribution, and also the point at which alcohol-alcohol hydrogen bonds become dominant over alcohol-water hydrogen bonds. Furthermore, the [Formula: see text] value showed transitions at 2.5 mol% 2-propanol and at approximately 14 mol% 2-propanol. Below 2.5 mol% 2-propanol the values of [Formula: see text] are negative; this is indicative of the presence of isolated 2-propanol molecules surrounded by water molecules. Above 2.5 mol% 2-propanol [Formula: see text] rises, reaching a maximum at ~14 mol% corresponding to a point where mixed alcohol-water networks are thought to dominate. The values and trends identified by PPC show excellent agreement not only with those obtained from MD simulations but also with results in the literature derived using viscometry, THz spectroscopy, NMR and neutron diffraction.

  4. Effect of bound state of water on hydronium ion mobility in hydrated Nafion using molecular dynamics simulations

    Energy Technology Data Exchange (ETDEWEB)

    Mabuchi, Takuya, E-mail: mabuchi@nanoint.ifs.tohoku.ac.jp [Graduate School of Engineering, Tohoku University, Sendai, Miyagi 980-8577 (Japan); Tokumasu, Takashi [Institute of Fluid Science, Tohoku University, Sendai, Miyagi 980-8577 (Japan)

    2014-09-14

    We have performed a detailed analysis of the structural properties of the sulfonate groups in terms of isolated and overlapped solvation shells in the nanostructure of hydrated Nafion membrane using classical molecular dynamics simulations. Our simulations have demonstrated the correlation between the two different areas in bound water region, i.e., the first solvation shell, and the vehicular transport of hydronium ions at different water contents. We have employed a model of the Nafion membrane using the improved force field, which is newly modified and validated by comparing the density and water diffusivity with those obtained experimentally. The first solvation shells were classified into the two types, the isolated area and the overlapped area. The mean residence times of solvent molecules explicitly showed the different behaviors in each of those areas in terms of the vehicular transport of protons: the diffusivity of classical hydronium ions in the overlapped area dominates their total diffusion at lower water contents while that in the isolated area dominates for their diffusion at higher water contents. The results provided insights into the importance role of those areas in the solvation shells for the diffusivity of vehicular transport of hydronium ions in hydrated Nafion membrane.

  5. Molecular Dynamics Simulations on the Behaviors of Hydrophilic/Hydrophobic Cyclic Peptide Nanotubes at the Water/Hexane Interface.

    Science.gov (United States)

    Lin, Huifang; Fan, Jianfen; Weng, Peipei; Si, Xialan; Zhao, Xin

    2017-09-08

    In this work, nine kinds of amino acid residues, i.e., alanine (A), leucine (L), valine (V), isoleucine (I), tryptophan (W), glutamine (Q), threonine (T), serine (S), and cysteine (C), were selected to construct seven cyclic peptide nanotubes (CPNTs) with diverse hydrophilic/hydrophobic external surfaces, which were further separately inserted at the water/hexane interface to investigate their microstructures and interfacial properties. Molecular dynamics (MD) simulations reveal that all the CPNTs except the QT- and VL-CPNTs have different degrees of tilt, fracture, and shedding at the interface. The end-CPs are more susceptible to the effect of the surroundings than the mid-CPs. The interactions of individual CP subunits with the neighborings disclose the firmness of the mid-CPs and the dissociation of the end-CPs. The results indicate that a hydrophobic CPNT is prone to stay at the interface, while a hydrophilic CPNT easily enters the water phase, resulting in many H-bonds with water. Results in this work enrich the dynamic properties of a hydrophilic/hydrophobic CPNT at the biphase interface at the atomic level.

  6. Quantum Corrections to Classical Molecular Dynamics Simulations of Water and Ice.

    Science.gov (United States)

    Waheed, Qaiser; Edholm, Olle

    2011-09-13

    Classical simulations of simple water models reproduce many properties of the liquid and ice but overestimate the heat capacity by about 65% at ordinary temperatures and much more for low temperature ice. This is due to the fact that the atomic vibrations are quantum mechanical. The application of harmonic quantum corrections to the molecular motion results in good heat capacities for the liquid and for ice at low temperatures but a successively growing positive deviation from experimental results for ice above 200 K that reaches 15% just below melting. We suggest that this deviation is due to the lack of quantum corrections to the anharmonic motions. For the liquid, the anharmonicities are even larger but also softer and thus in less need of quantum correction. Therefore, harmonic quantum corrections to the classically calculated liquid heat capacities result in agreement with the experimental values. The classical model underestimates the heat of melting by 15%, while the application of quantum corrections produces fair agreement. On the other hand, the heat of vaporization is overestimated by 10% in the harmonically corrected classical model.

  7. Structure, dynamics, and function of the hammerhead ribozyme in bulk water and at a clay mineral surface from replica exchange molecular dynamics.

    Science.gov (United States)

    Swadling, Jacob B; Wright, David W; Suter, James L; Coveney, Peter V

    2015-03-01

    Compared with proteins, the relationship between structure, dynamics, and function of RNA enzymes (known as ribozymes) is far less well understood, despite the fact that ribozymes are found in many organisms and are often conceived as "molecular fossils" of the first self-replicating molecules to have arisen on Earth. To investigate how ribozymal function is governed by structure and dynamics, we study the full hammerhead ribozyme in bulk water and in an aqueous clay mineral environment by computer simulation using replica-exchange molecular dynamics. Through extensive sampling of the major conformational states of the hammerhead ribozyme, we are able to show that the hammerhead manifests a free-energy landscape reminiscent of that which is well known in proteins, exhibiting a "funnel" topology that guides the ribozyme into its globally most stable conformation. The active-site geometry is found to be closely correlated to the tertiary structure of the ribozyme, thereby reconciling conflicts between previously proposed mechanisms for the self-scission of the hammerhead. The conformational analysis also accounts for the differences reported experimentally in the catalytic activity of the hammerhead ribozyme, which is reduced when interacting with clay minerals as compared with bulk water.

  8. STRUCTURAL-PROPERTIES OF 1,2-DIACYL-SN-GLYCEROL IN BULK AND AT THE WATER INTERFACE BY MOLECULAR-DYNAMICS

    NARCIS (Netherlands)

    VANBUUREN, AR; DEVLIEG, J; BERENDSEN, HJC

    1995-01-01

    We performed four different molecular dynamics (MD) simulations of 1,2-dilauroyl-sn-glycerol (DLG) systems at 300 and 360 K: a crystal simulation, a pure DLG oil phase, a DLG oil phase in contact with a water layer, and an oil/monolayer/water simulation. All these systems were simulated for several

  9. Reactivity of aldehydes at the air-water interface. Insights from molecular dynamics simulations and ab initio calculations.

    Science.gov (United States)

    Martins-Costa, Marilia T C; García-Prieto, Francisco F; Ruiz-López, Manuel F

    2015-02-14

    Understanding the influence of solute-solvent interactions on chemical reactivity has been a subject of intense research in the last few decades. Theoretical studies have focused on bulk solvation phenomena and a variety of models and methods have been developed that are now widely used by both theoreticians and experimentalists. Much less attention has been paid, however, to processes that occur at liquid interfaces despite the important role such interfaces play in chemistry and biology. In this study, we have carried out sequential molecular dynamics simulations and quantum mechanical calculations to analyse the influence of the air-water interface on the reactivity of formaldehyde, acetaldehyde and benzaldehyde, three simple aldehydes of atmospheric interest. The calculated free-energy profiles exhibit a minimum at the interface, where the average reactivity indices may display large solvation effects. The study emphasizes the role of solvation dynamics, which are responsible for large fluctuations of some molecular properties. We also show that the photolysis rate constant of benzaldehyde in the range 290-308 nm increases by one order of magnitude at the surface of a water droplet, from 2.7 × 10(-5) s(-1) in the gas phase to 2.8 × 10(-4) s(-1) at the air-water interface, and we discuss the potential impact of this result on the chemistry of the troposphere. Experimental data in this domain are still scarce and computer simulations like those presented in this work may provide some insights that can be useful to design new experiments.

  10. Molecular dynamics simulation of water/BHDC cationic reverse micelles. structural characterization, dynamical properties, and influence of solvent on intermicellar interactions.

    Science.gov (United States)

    Agazzi, Federico M; Correa, N Mariano; Rodriguez, Javier

    2014-08-19

    We report results obtained from molecular dynamics (MD) experiments of benzylhexadecyldimethylammonium chloride (BHDC) cationic reverse micelles (RMs). In particular we analyzed equilibrium and dynamical characteristics of water/BHDC RMs in pure benzene, at two different water/BHDC ratios (W0 = 5 and W0 = 10). The RMs appear as elliptical aggregates with eccentricities close to ∼0.9. Analysis of the different spatial correlations reveals three different spatial domains in the RMs: a water inner pool, the surfactant interface, and the external solvent. The calculated accessible surface areas for the aqueous inner cores suggest a strong penetration of solvent molecules within the micellar interface domains. Comparison between the density profiles of both RMs shows an increment of the broadness in the distributions of all species at the interface, along with an increasing overlap between the tail segments of the surfactant and benzene molecules as one considers larger micelles. For the dynamical side, the rotational characteristic time scale for the confined water was found to be 1 order of magnitude larger than that of the bulk water. A similar effect was also observed for hydrogen bond dynamics. Both retardation effects diminish with the size of the aggregate. To the estimate the influence of the external solvent on the intermicellar interactions, free energy profiles for the coalescence process between RMs of similar size in pure benzene and in a n-heptane/benzene mixture were also investigated. The results indicate that the association process is facilitated by the presence of n-heptane in the external nonpolar phase. Comparison with previous theoretical and experimental results is also carried out.

  11. Simulations of light induced processes in water based on ab initio path integrals molecular dynamics. II. Photoionization

    Science.gov (United States)

    Svoboda, Ondřej; Ončák, Milan; Slavíček, Petr

    2011-10-01

    We have applied ab initio based reflection principle to simulate photoelectron spectra of small water clusters, ranging from monomer to octamer. The role of quantum and thermal effects on the structure of the water photoelectron spectra is discussed within the ab initio path integral molecular dynamics (PIMD) framework. We have used the PIMD method with up to 40 beads to sample the ground state quantum distribution at temperature T = 180 K. We have thoroughly tested the performance of various density functionals (B3LYP, BHandHLYP, M06HF, BNL, LC-ωPBE, and CAM-B3LYP) for the ionization process description. The benchmarking based on a comparison of simulated photoelectron spectra to experimental data and high level equation-of-motion ionization potential coupled clusters with singles and doubles calculations has singled out the BHandHLYP and LC-ωPBE functionals as the most reliable ones for simulations of light induced processes in water. The good performance of the density functional theory functionals to model the water photoelectron spectra also reflects their ability to reliably describe open shell excited states. The width of the photoelectron spectrum converges quickly with the cluster size as it is controlled by specific interactions of local character. The peak position is, on the other hand, defined by long-range non-specific solvent effects; it therefore only slowly converges to the corresponding bulk value. We are able to reproduce the experimental valence photoelectron spectrum of liquid water within the combined model of the water octamer embedded in a polarizable dielectric continuum. We demonstrate that including the long-range polarization and the state-specific treatment of the solvent response are needed for a reliable liquid water ionization description.

  12. Structure and energetics of model amphiphilic molecules at the water liquid-vapor interface - A molecular dynamics study

    Science.gov (United States)

    Pohorille, Andrew; Benjamin, Ilan

    1993-01-01

    A molecular dynamics study of adsorption of p-n-pentylphenol at infinite dilution at the water liquid-vapor interface is reported. The calculated free energy of adsorption is -8.8 +/- 0.7 kcal/mol, in good agreement with the experimental value of -7.3 kcal/mol. The transition between the interfacial region and the bulk solution is sharp and well-defined by energetic, conformational, and orientational criteria. At the water surface, the phenol head group is mostly immersed in aqueous solvent. The most frequent orientation of the hydrocarbon tail is parallel to the interface, due to dispersion interactions with the water surface. This arrangement of the phenol ring and the alkyl chain requires that the chain exhibits a kink. As the polar head group is being moved into the solvent, the chain length increases and the tail becomes increasingly aligned toward the surface normal, such that the nonpolar part of the molecule exposed to water is minimized. The same effect was achieved when phenol was replaced by a more polar head group, phenolate.

  13. Structure and energetics of model amphiphilic molecules at the water liquid-vapor interface - A molecular dynamics study

    Science.gov (United States)

    Pohorille, Andrew; Benjamin, Ilan

    1993-01-01

    A molecular dynamics study of adsorption of p-n-pentylphenol at infinite dilution at the water liquid-vapor interface is reported. The calculated free energy of adsorption is -8.8 +/- 0.7 kcal/mol, in good agreement with the experimental value of -7.3 kcal/mol. The transition between the interfacial region and the bulk solution is sharp and well-defined by energetic, conformational, and orientational criteria. At the water surface, the phenol head group is mostly immersed in aqueous solvent. The most frequent orientation of the hydrocarbon tail is parallel to the interface, due to dispersion interactions with the water surface. This arrangement of the phenol ring and the alkyl chain requires that the chain exhibits a kink. As the polar head group is being moved into the solvent, the chain length increases and the tail becomes increasingly aligned toward the surface normal, such that the nonpolar part of the molecule exposed to water is minimized. The same effect was achieved when phenol was replaced by a more polar head group, phenolate.

  14. Simulations of light induced processes in water based on ab initio path integrals molecular dynamics. I. Photoabsorption

    Science.gov (United States)

    Svoboda, Ondřej; Ončák, Milan; Slavíček, Petr

    2011-10-01

    We have performed large-scale simulations of UV absorption spectra of water clusters (monomer to octamer) using a combination of ab initio path-integral molecular dynamics with reflection principle. The aim of the present work is four-fold: (1) To explore the transition from isolated molecules to bulk water from the perspective of UV photoabsorption. (2) To investigate quantum nuclear and thermal effects on the shape of the water UV spectra. (3) To make an assessment of the density functional theory functionals to be used for water excited states. (4) To check the applicability of the QM/MM schemes for a description of the UV absorption. Within the path integral molecular dynamics (PIMD)/reflection principle approach both the thermal and quantum vibrational effects including anharmonicities are accounted for. We demonstrate that shape of the spectra is primarily controlled by the nuclear quantum effects. The excited states and transition characteristics of the water clusters were calculated with the time-dependent density functional theory and equation-of-motion coupled clusters singles and doubles methods. Based on our benchmark calculations considering the whole UV spectrum we argue that the BHandHLYP method performs best among the 6 functionals tested (B3LYP, BHandHLYP, BNL, CAM-B3LYP, LC-ωPBE, and M06HF). We observe a gradual blueshift of the maximum of the first absorption peak with the increasing cluster size. The UV absorption spectrum for the finite size clusters (i.e., the peak centers, peak widths, and photoabsorption cross section) essentially converges into the corresponding bulk water spectrum. The effect of distant molecules accounted for within the polarizable continuum model is shown to be almost negligible. Using the natural transition orbitals we demonstrate that the first absorption band is formed by localized excitations while the second band includes delocalized excited states. Consequently, the QM/MM electrostatic embedding scheme can only be

  15. Grand canonical Molecular Dynamics Simulations

    CERN Document Server

    Fritsch, S; Junghans, C; Ciccotti, G; Site, L Delle; Kremer, K

    2011-01-01

    For simulation studies of (macro-) molecular liquids it would be of significant interest to be able to adjust/increase the level of resolution within one region of space, while allowing for the free exchange of molecules between (open) regions of different resolution/representation. In the present work we generalize the adaptive resolution idea in terms of a generalized Grand Canonical approach. This provides a robust framework for truly open Molecular Dynamics systems. We apply the method to liquid water at ambient conditions.

  16. Molecular water oxidation catalysis

    CERN Document Server

    Llobet, Antoni

    2014-01-01

    Photocatalytic water splitting is a promising strategy for capturing energy from the sun by coupling light harvesting and the oxidation of water, in order to create clean hydrogen fuel. Thus a deep knowledge of the water oxidation catalysis field is essential to be able to come up with useful energy conversion devices based on sunlight and water splitting. Molecular Water Oxidation Catalysis: A Key Topic for New Sustainable Energy Conversion Schemes presents a comprehensive and state-of-the-art overview of water oxidation catalysis in homogeneous phase, describing in detail the most importan

  17. Path integral molecular dynamics within the grand canonical-like adaptive resolution technique: Simulation of liquid water

    Energy Technology Data Exchange (ETDEWEB)

    Agarwal, Animesh, E-mail: animesh@zedat.fu-berlin.de; Delle Site, Luigi, E-mail: dellesite@fu-berlin.de [Institute for Mathematics, Freie Universität Berlin, Berlin (Germany)

    2015-09-07

    Quantum effects due to the spatial delocalization of light atoms are treated in molecular simulation via the path integral technique. Among several methods, Path Integral (PI) Molecular Dynamics (MD) is nowadays a powerful tool to investigate properties induced by spatial delocalization of atoms; however, computationally this technique is very demanding. The above mentioned limitation implies the restriction of PIMD applications to relatively small systems and short time scales. One of the possible solutions to overcome size and time limitation is to introduce PIMD algorithms into the Adaptive Resolution Simulation Scheme (AdResS). AdResS requires a relatively small region treated at path integral level and embeds it into a large molecular reservoir consisting of generic spherical coarse grained molecules. It was previously shown that the realization of the idea above, at a simple level, produced reasonable results for toy systems or simple/test systems like liquid parahydrogen. Encouraged by previous results, in this paper, we show the simulation of liquid water at room conditions where AdResS, in its latest and more accurate Grand-Canonical-like version (GC-AdResS), is merged with two of the most relevant PIMD techniques available in the literature. The comparison of our results with those reported in the literature and/or with those obtained from full PIMD simulations shows a highly satisfactory agreement.

  18. Path integral molecular dynamics within the grand canonical-like adaptive resolution technique: Simulation of liquid water

    Science.gov (United States)

    Agarwal, Animesh; Delle Site, Luigi

    2015-09-01

    Quantum effects due to the spatial delocalization of light atoms are treated in molecular simulation via the path integral technique. Among several methods, Path Integral (PI) Molecular Dynamics (MD) is nowadays a powerful tool to investigate properties induced by spatial delocalization of atoms; however, computationally this technique is very demanding. The above mentioned limitation implies the restriction of PIMD applications to relatively small systems and short time scales. One of the possible solutions to overcome size and time limitation is to introduce PIMD algorithms into the Adaptive Resolution Simulation Scheme (AdResS). AdResS requires a relatively small region treated at path integral level and embeds it into a large molecular reservoir consisting of generic spherical coarse grained molecules. It was previously shown that the realization of the idea above, at a simple level, produced reasonable results for toy systems or simple/test systems like liquid parahydrogen. Encouraged by previous results, in this paper, we show the simulation of liquid water at room conditions where AdResS, in its latest and more accurate Grand-Canonical-like version (GC-AdResS), is merged with two of the most relevant PIMD techniques available in the literature. The comparison of our results with those reported in the literature and/or with those obtained from full PIMD simulations shows a highly satisfactory agreement.

  19. A Comprehensive Study of Hydrogen Adsorbing to Amorphous Water-Ice: Defining Adsorption in Classical Molecular Dynamics

    CERN Document Server

    Dupuy, John L; Stancil, P C

    2016-01-01

    Gas-grain and gas-phase reactions dominate the formation of molecules in the interstellar medium (ISM). Gas-grain reactions require a substrate (e.g. a dust or ice grain) on which the reaction is able to occur. The formation of molecular hydrogen (H$_2$) in the ISM is the prototypical example of a gas-grain reaction. In these reactions, an atom of hydrogen will strike a surface, stick to it, and diffuse across it. When it encounters another adsorbed hydrogen atom, the two can react to form molecular hydrogen and then be ejected from the surface by the energy released in the reaction. We perform in-depth classical molecular dynamics (MD) simulations of hydrogen atoms interacting with an amorphous water-ice surface. This study focuses on the first step in the formation process; the sticking of the hydrogen atom to the substrate. We find that careful attention must be paid in dealing with the ambiguities in defining a sticking event. The technical definition of a sticking event will affect the computed sticking ...

  20. Molecular Dynamics Simulation Study of Parallel Telomeric DNA Quadruplexes at Different Ionic Strengths: Evaluation of Water and Ion Models.

    Science.gov (United States)

    Rebič, Matúš; Laaksonen, Aatto; Šponer, Jiří; Uličný, Jozef; Mocci, Francesca

    2016-08-04

    Most molecular dynamics (MD) simulations of DNA quadruplexes have been performed under minimal salt conditions using the Åqvist potential parameters for the cation with the TIP3P water model. Recently, this combination of parameters has been reported to be problematic for the stability of quadruplex DNA, especially caused by the ion interactions inside or near the quadruplex channel. Here, we verify how the choice of ion parameters and water model can affect the quadruplex structural stability and the interactions with the ions outside the channel. We have performed a series of MD simulations of the human full-parallel telomeric quadruplex by neutralizing its negative charge with K(+) ions. Three combinations of different cation potential parameters and water models have been used: (a) Åqvist ion parameters, TIP3P water model; (b) Joung and Cheatham ion parameters, TIP3P water model; and (c) Joung and Cheatham ion parameters, TIP4Pew water model. For the combinations (b) and (c), the effect of the ionic strength has been evaluated by adding increasing amounts of KCl salt (50, 100, and 200 mM). Two independent simulations using the Åqvist parameters with the TIP3P model show that this combination is clearly less suited for the studied quadruplex with K(+) as counterions. In both simulations, one ion escapes from the channel, followed by significant deformation of the structure, leading to deviating conformation compared to that in the reference crystallographic data. For the other combinations of ion and water potentials, no tendency is observed for the channel ions to escape from the quadruplex channel. In addition, the internal mobility of the three loops, torsion angles, and counterion affinity have been investigated at varied salt concentrations. In summary, the selection of ion and water models is crucial as it can affect both the structure and dynamics as well as the interactions of the quadruplex with its counterions. The results obtained with the TIP4Pew

  1. Temperature and isotope effects on water cluster ions with path integral molecular dynamics based on the fourth order Trotter expansion

    Science.gov (United States)

    Suzuki, Kimichi; Shiga, Motoyuki; Tachikawa, Masanori

    2008-10-01

    Path integral molecular dynamics simulation based on the fourth order Trotter expansion has been performed to elucidate the geometrical isotope effect of water dimer anions, H3O2-, D3O2-, and T3O2-, at different temperatures from 50 to 600 K. At low temperatures below 200 K the hydrogen-bonded hydrogen nucleus is near the center of two oxygen atoms with mostly O⋯X⋯O geometry (where X =H, D, or T), while at high temperatures above 400 K, hydrogen becomes more delocalized, showing the coexistence between O⋯X-O and O-X⋯O. The OO distance tends to be shorter as the isotopomer is heavier at low temperatures, while this ordering becomes opposite at high temperatures. It is concluded that the coupling between the OO stretching mode and proton transfer modes is a key to understand such a temperature dependence of a hydrogen-bonded structure.

  2. A rain induced landslide 3D model based on molecular dynamics with fractal and fractional water diffusion

    CERN Document Server

    Martelloni, Gianluca; Guarino, Alessio

    2016-01-01

    We present a three-dimensional model, based on cohesive spherical particles, of rain-induced landslides. The rainwater infiltration into the soil follow the either the fractional or the fractal diffusion equations. We solve analytically the fractal diffusion partial differential equation (PDE) with particular boundary conditions to simulate a rainfall event. Then, for the PDE, we developed a numerical integration scheme that we integrate with MD (Molecular Dynamics) algorithm for the triggering and propagation of the simulated landslide. Therefore we test the numerical integration scheme of fractal diffusion equation with the analytical solution. We adopt the fractal diffusion equation in term of gravimetric water content that we use as input of triggering scheme based on Mohr-Coulomb limit-equilibrium criterion, adapted to particle level. Moreover, taking into account an interacting force Lennard-Jones inspired, we use a standard MD algorithm to update particle positions and velocities. Then we present resul...

  3. Algorithms for GPU-based molecular dynamics simulations of complex fluids: Applications to water, mixtures, and liquid crystals.

    Science.gov (United States)

    Kazachenko, Sergey; Giovinazzo, Mark; Hall, Kyle Wm; Cann, Natalie M

    2015-09-15

    A custom code for molecular dynamics simulations has been designed to run on CUDA-enabled NVIDIA graphics processing units (GPUs). The double-precision code simulates multicomponent fluids, with intramolecular and intermolecular forces, coarse-grained and atomistic models, holonomic constraints, Nosé-Hoover thermostats, and the generation of distribution functions. Algorithms to compute Lennard-Jones and Gay-Berne interactions, and the electrostatic force using Ewald summations, are discussed. A neighbor list is introduced to improve scaling with respect to system size. Three test systems are examined: SPC/E water; an n-hexane/2-propanol mixture; and a liquid crystal mesogen, 2-(4-butyloxyphenyl)-5-octyloxypyrimidine. Code performance is analyzed for each system. With one GPU, a 33-119 fold increase in performance is achieved compared with the serial code while the use of two GPUs leads to a 69-287 fold improvement and three GPUs yield a 101-377 fold speedup.

  4. Strong electric fields at a prototypical oxide/water interface probed by ab initio molecular dynamics: MgO(001).

    Science.gov (United States)

    Laporte, Sara; Finocchi, Fabio; Paulatto, Lorenzo; Blanchard, Marc; Balan, Etienne; Guyot, François; Saitta, Antonino Marco

    2015-08-21

    We report a density-functional theory (DFT)-based study of the interface of bulk water with a prototypical oxide surface, MgO(001), and focus our study on the often-overlooked surface electric field. In particular, we observe that the bare MgO(001) surface, although charge-neutral and defectless, has an intense electric field on the Å scale. The MgO(001) surface covered with 1 water monolayer (1 ML) is investigated via a supercell accounting for the experimentally-observed (2 × 3) reconstruction, stable at ambient temperature, and in which two out of six water molecules are dissociated. This 1 ML-hydrated surface is also found to have a high, albeit short-ranged, normal component of the field. Finally, the oxide/water interface is studied via room-temperature ab initio molecular dynamics (AIMD) using 34 H2O molecules between two MgO(001) surfaces. To our best knowledge this is the first AIMD study of the MgO(001)/liquid water interface in which all atoms are treated using DFT and including several layers above the first adsorbed layer. We observe that the surface electric field, averaged over the AIMD trajectories, is still very strong on the fully-wet surface, peaking at about 3 V Å(-1). Even in the presence of bulk-like water, the structure of the first layer in contact with the surface remains similar to the (2 × 3)-reconstructed ice ad-layer on MgO(001). Moreover, we observe proton exchange within the first layer, and between the first and second layers - indeed, the O-O distances close to the surface are found to be distributed towards shorter distances, a property which has been shown to directly promote proton transfer.

  5. Molecular Dynamics Simulation of Atomic Force Microscopy at the Water-Muscovite Interface: Hydration Layer Structure and Force Analysis.

    Science.gov (United States)

    Kobayashi, Kazuya; Liang, Yunfeng; Amano, Ken-ichi; Murata, Sumihiko; Matsuoka, Toshifumi; Takahashi, Satoru; Nishi, Naoya; Sakka, Tetsuo

    2016-04-19

    With the development of atomic force microscopy (AFM), it is now possible to detect the buried liquid-solid interfacial structure in three dimensions at the atomic scale. One of the model surfaces used for AFM is the muscovite surface because it is atomically flat after cleavage along the basal plane. Although it is considered that force profiles obtained by AFM reflect the interfacial structures (e.g., muscovite surface and water structure), the force profiles are not straightforward because of the lack of a quantitative relationship between the force and the interfacial structure. In the present study, molecular dynamics simulations were performed to investigate the relationship between the muscovite-water interfacial structure and the measured AFM force using a capped carbon nanotube (CNT) AFM tip. We provide divided force profiles, where the force contributions from each water layer at the interface are shown. They reveal that the first hydration layer is dominant in the total force from water even after destruction of the layer. Moreover, the lateral structure of the first hydration layer transcribes the muscovite surface structure. It resembles the experimentally resolved surface structure of muscovite in previous AFM studies. The local density profile of water between the tip and the surface provides further insight into the relationship between the water structure and the detected force structure. The detected force structure reflects the basic features of the atomic structure for the local hydration layers. However, details including the peak-peak distance in the force profile (force-distance curve) differ from those in the density profile (density-distance curve) because of disturbance by the tip.

  6. Reactive molecular dynamics of the initial oxidation stages of Ni111 in pure water: effect of an applied electric field.

    Science.gov (United States)

    Assowe, O; Politano, O; Vignal, V; Arnoux, P; Diawara, B; Verners, O; van Duin, A C T

    2012-12-01

    Corrosion processes occurring in aqueous solutions are critically dependent upon the interaction between the metal electrode and the solvent. In this work, the interaction of a nickel substrate with water molecules has been investigated using reactive force field (ReaxFF) molecular dynamics simulations. This approach was originally developed by van Duin and co-workers to study hydrocarbon chemistry and the catalytic properties of organic compounds. To our knowledge, this method has not previously been used to study the corrosion of nickel. In this work, we studied the interaction of 480 molecules of water (ρ = 0.99 g·cm(-3)) with Ni(111) surfaces at 300 K. The results showed that a water "bilayer" was adsorbed on the nickel surface. In the absence of an applied electric field, no dissociation of water was observed. However, the nickel atoms at the surface were charged positively, whereas the first water layer was charged negatively, indicating the formation of an electric double layer. To study the corrosion of nickel in pure water, we introduced an external electric field between the metal and the solution. The electric field intensity varied between 10 and 20 MeV/cm. The presence of this electric field led to oxidation of the metal surface. The structural and morphological differences associated with the growth of this oxide film in the presence of the electric field were evaluated. The simulated atomic trajectories were used to analyze the atomic displacement during the reactive process. The growth of the oxide scale on the nickel surface was primarily due to the movement of anions toward the interior of the metal substrate and the migration of nickel toward the free surface. We found that increasing the electric field intensity sped up the corrosion of nickel. The results also showed that the oxide film thickness increased linearly with increasing electric field intensity.

  7. Molecular Dynamics Studies on Liquid/Vapor Interface Properties and Structures of 1-Ethyl-3-methylimidazolium Dimethylphosphate-Water.

    Science.gov (United States)

    Li, Tianyu; Zhao, Zongchang; Zhang, Xiaodong; Sun, Xican

    2017-04-13

    1-Ethyl-3-methylimidazolium dimethylphosphate ([Emim][Dmp])-water binary solution is one of the promising new working-pairs for absorption heat pump and absorption chillers, which are widely used to recover industrial waste heat. In the absorption process, the mass and heat transfer at the interface greatly depend on interface microscopic structure. Therefore, in order to understand the absorption process, it is very important to study the interface microscopic structure. The liquid-vapor interface properties, as well as the orientation of [Emim](+), [Dmp](-), water at the interface and its aqueous solution with different water mole fraction, were studied using classical all-atom force field by molecular dynamic simulations. The simulated bulk mass density fitted by hyperbolic tangent function for each system was in good agreement with the experiment data, with the relative deviation between simulated and experimental value within 2%. The simulated results indicate that anion is always distributed at the outmost layer of the interface, followed by cation and water molecule. In [Emim][Dmp], the tilt angle of imidazolium rings to the surface normal is in the range of 0° interface, but almost all ethyl intend to tilt toward gas phase and the methyl tilt toward liquid bulk compared with pure [Emim][Dmp]. Two methyl in anion prefer to turn toward gas phase and its two PO vectors toward liquid bulk. This orientation indicates that pure [Emim][Dmp] absorb water in gas phase more easily than [Emim][Dmp]+H2O system does. Water molecules are distributed in the inner layer of the interface with two OH vectors (from O atom to H atom) tilting toward external surface.

  8. Molecular dynamics simulations of LiCl association and NaCl association in water by means of ABEEM/MM

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    Constrained molecular dynamics simulations have been used to investigate the LiCl and NaCl ionic association in water in terms of atom-bond electronegativity equalization method fused into molecular mechanics (ABEEM/MM). The simulations make use of the seven-site fluctuating charge and flexible ABEEM-7P water model, based on which an ion-water interaction potential has been constructed. The mean force and the potential of mean force for LiCl and NaCl in water, the charge distributions, as well as the structural and dynamical properties of contact ion pair dissociation have been investigated. The results are reasonable and informative. For LiCl ion pair in water, the solvent-separated ion pair configurations are more stable than contact ion pair configurations. The calculated PMF for NaCl in water indicates that contact ion pair and solvent-separated ion pair configurations are of comparable stability.

  9. Relationship between structural order and water-like anomalies in metastable liquid silicon: Ab initio molecular dynamics

    Science.gov (United States)

    Zhao, G.; Yan, J. L.; Yu, Y. J.; Ding, M. C.; Zhao, X. G.; Wang, H. Y.

    2017-01-01

    The relationship between structural order and water-like anomalies in tetrahedral liquids is still open. Here, first-principle molecular dynamics are performed to study it in metastable liquid Si. It is found that in T-P phase diagram, there indeed exists a structural anomaly region, which encloses density anomaly but not diffusivity anomaly. This is consistent with that of SW Si and BKS SiO2 but different from that of SPC/E water. Two-body excess entropy anomaly can neither capture the diffusivity, structural, and density anomalies, as it can in a two-scale potential fluid. In structural anomaly region, tetrahedrality order qtetra (measuring the extent to which an atom and its four nearest neighbours adopt tetrahedral arrangement) and translational order ttrans (measuring the tendency of two atoms to adopt preferential separation) are not perfectly correlated, which is different from that in SW Si and renders it impossible to use the isotaxis line to quantify the degree of structural order needed for water-like anomalies to occur. Along the isotherm of critical temperature Tc, ttrans/qtetra is approximately linear with pressure. With decreasing pressure along the isotherm below Tc, ttrans/qtetra departs downward from the line, while it is the opposite case above Tc.

  10. Molecular Dynamics Simulation of Na(+)-Cl(-) Ion-Pair in Water-Methanol Mixtures under Supercritical and Ambient Conditions.

    Science.gov (United States)

    Keshri, Sonanki; Sarkar, Atanu; Tembe, B L

    2015-12-17

    Constrained molecular dynamics simulations have been performed to investigate the structure and thermodynamics of Na(+)-Cl(-) ion-pair association in water-methanol mixtures under supercritical and ambient conditions in dilute solutions. From the computed potentials of mean force (PMFs) we find that contact ion pairs (CIPs) are more stable than all other associated states of the ion pairs in both ambient and supercritical conditions. Stabilities of CIPs increase with increase in the mole fraction of methanol. In supercritical conditions, major changes in PMFs occur as we go from x(methanol) = 0.00 to x(methanol) = 0.50. The stable solvent shared ion pair (SShIP) which occurs in x(methanol) = 0.00 and 0.25, vanishes when x(methanol) is 0.50 or greater. The stabilities of these ion pairs increase with increasing temperature. Local structures around the ions are studied using the radial distribution functions, density profiles, angular distribution functions, running coordination numbers and excess coordination numbers. Preferential solvation analysis shows that both Na(+) and Cl(-) ions are preferentially solvated by water. From the calculation of enthalpies and entropies, we find that Na(+)-Cl(-) ion-pair association in water-methanol binary mixtures is endothermic and driven by entropy both in ambient as well as under supercritical conditions.

  11. Relationship between structural order and water-like anomalies in metastable liquid silicon: Ab initio molecular dynamics

    Science.gov (United States)

    Zhao, G.; Yan, J. L.; Yu, Y. J.; Ding, M. C.; Zhao, X. G.; Wang, H. Y.

    2017-01-01

    The relationship between structural order and water-like anomalies in tetrahedral liquids is still open. Here, first-principle molecular dynamics are performed to study it in metastable liquid Si. It is found that in T-P phase diagram, there indeed exists a structural anomaly region, which encloses density anomaly but not diffusivity anomaly. This is consistent with that of SW Si and BKS SiO2 but different from that of SPC/E water. Two-body excess entropy anomaly can neither capture the diffusivity, structural, and density anomalies, as it can in a two-scale potential fluid. In structural anomaly region, tetrahedrality order qtetra (measuring the extent to which an atom and its four nearest neighbours adopt tetrahedral arrangement) and translational order ttrans (measuring the tendency of two atoms to adopt preferential separation) are not perfectly correlated, which is different from that in SW Si and renders it impossible to use the isotaxis line to quantify the degree of structural order needed for water-like anomalies to occur. Along the isotherm of critical temperature Tc, ttrans/qtetra is approximately linear with pressure. With decreasing pressure along the isotherm below Tc, ttrans/qtetra departs downward from the line, while it is the opposite case above Tc. PMID:28054595

  12. Theoretical Characterization of the Spectral Density of the Water-Soluble Chlorophyll-Binding Protein from Combined Quantum Mechanics/Molecular Mechanics Molecular Dynamics Simulations.

    Science.gov (United States)

    Rosnik, Andreana M; Curutchet, Carles

    2015-12-08

    Over the past decade, both experimentalists and theorists have worked to develop methods to describe pigment-protein coupling in photosynthetic light-harvesting complexes in order to understand the molecular basis of quantum coherence effects observed in photosynthesis. Here we present an improved strategy based on the combination of quantum mechanics/molecular mechanics (QM/MM) molecular dynamics (MD) simulations and excited-state calculations to predict the spectral density of electronic-vibrational coupling. We study the water-soluble chlorophyll-binding protein (WSCP) reconstituted with Chl a or Chl b pigments as the system of interest and compare our work with data obtained by Pieper and co-workers from differential fluorescence line-narrowing spectra (Pieper et al. J. Phys. Chem. B 2011, 115 (14), 4042-4052). Our results demonstrate that the use of QM/MM MD simulations where the nuclear positions are still propagated at the classical level leads to a striking improvement of the predicted spectral densities in the middle- and high-frequency regions, where they nearly reach quantitative accuracy. This demonstrates that the so-called "geometry mismatch" problem related to the use of low-quality structures in QM calculations, not the quantum features of pigments high-frequency motions, causes the failure of previous studies relying on similar protocols. Thus, this work paves the way toward quantitative predictions of pigment-protein coupling and the comprehension of quantum coherence effects in photosynthesis.

  13. Coarse-grained molecular dynamics simulation of water diffusion in the presence of carbon nanotubes.

    Science.gov (United States)

    Lado Touriño, Isabel; Naranjo, Arisbel Cerpa; Negri, Viviana; Cerdán, Sebastián; Ballesteros, Paloma

    2015-11-01

    Computational modeling of the translational diffusion of water molecules in anisotropic environments entails vital relevance to understand correctly the information contained in the magnetic resonance images weighted in diffusion (DWI) and of the diffusion tensor images (DTI). In the present work we investigated the validity, strengths and weaknesses of a coarse-grained (CG) model based on the MARTINI force field to simulate water diffusion in a medium containing carbon nanotubes (CNTs) as models of anisotropic water diffusion behavior. We show that water diffusion outside the nanotubes follows Ficḱs law, while water diffusion inside the nanotubes is not described by a Ficḱs behavior. We report on the influence on water diffusion of various parameters such as length and concentration of CNTs, comparing the CG results with those obtained from the more accurate classic force field calculation, like the all-atom approach. Calculated water diffusion coefficients decreased in the presence of nanotubes in a concentration dependent manner. We also observed smaller water diffusion coefficients for longer CNTs. Using the CG methodology we were able to demonstrate anisotropic diffusion of water inside the nanotube scaffold, but we could not prove anisotropy in the surrounding medium, suggesting that grouping several water molecules in a single diffusing unit may affect the diffusional anisotropy calculated. The methodologies investigated in this work represent a first step towards the study of more complex models, including anisotropic cohorts of CNTs or even neuronal axons, with reasonable savings in computation time.

  14. Molecular origin of drug release by water boiling inside carbon nanotubes from reactive molecular dynamics simulation and DFT perspectives.

    Science.gov (United States)

    Ganji, M Darvish; Mirzaei, Sh; Dalirandeh, Z

    2017-07-05

    Owing to their nanosized hollow cylindrical structure, CNTs hold the promise to be utilized as desired materials for encapsulating molecules which demonstrate wide inferences in drug delivery. Here we evaluate the possibility of drug release from the CNTs with various types and edge chemistry by reactive MD simulation to explain the scientifically reliable relations for proposed process. It was shown that heating of CNTs (up to 750 K) cannot be used for release of incorporated drug (phenylalanine) into water and even carbonated water solvent with very low boiling temperature. This is due to the strong physisorption (π-stacking interaction) between the aromatic of encapsulated drug and CNT sidewall which causes the drug to bind the nanotube sidewall. We have further investigated the interaction nature and release mechanism of water and drug confined/released within/from the CNTs by DFT calculations and the results confirmed our MD simulation findings. The accuracy of DFT method was also validated against the experimental and theoretical values at MP2/CCSD level. Therefore, we find that boiling of water/carbonated water confined within the CNTs could not be a suitable technique for efficient drug release. Our atomistic simulations provide a well-grounded understanding for the release of drug molecules confined within CNTs.

  15. Effect of Surface Oxidation on Interfacial Water Structure at a Pyrite (100) Surface as Studied by Molecular Dynamics Simulation

    Energy Technology Data Exchange (ETDEWEB)

    Jin, Jiaqi; Miller, Jan D.; Dang, Liem X.; Wick, Collin D.

    2015-06-01

    In the first part of this paper, a Scanning Electron Microscopy and contact angle study of a pyrite surface (100) is reported describing the relationship between surface oxidation and the hydrophilic surface state. In addition to these experimental results, the following simulated surface states were examined using Molecular Dynamics Simulation (MDS): fresh unoxidized (100) surface; polysulfide at the (100) surface; elemental sulfur at the (100) surface. Crystal structures for the polysulfide and elemental sulfur at the (100) surface were simulated using Density Functional Theory (DFT) quantum chemical calculations. The well known oxidation mechanism which involves formation of a metal deficient layer was also described with DFT. Our MDS results of the behavior of interfacial water at the fresh and oxidized pyrite (100) surfaces without/with the presence of ferric hydroxide include simulated contact angles, number density distribution for water, water dipole orientation, water residence time, and hydrogen-bonding considerations. The significance of the formation of ferric hydroxide islands in accounting for the corresponding hydrophilic surface state is revealed not only from experimental contact angle measurements but also from simulated contact angle measurements using MDS. The hydrophilic surface state developed at oxidized pyrite surfaces has been described by MDS, on which basis the surface state is explained based on interfacial water structure. The Division of Chemical Sciences, Geosciences, and Biosciences, Office of Basic Energy Sciences (BES), of the DOE funded work performed by Liem X. Dang. Battelle operates the Pacific Northwest National Laboratory for DOE. The calculations were carried out using computer resources provided by BES.

  16. Density dependence of the entropy and the solvation shell structure in supercritical water via molecular dynamics simulation.

    Science.gov (United States)

    Ma, Haibo

    2012-06-07

    We perform molecular dynamics simulations of supercritical water (SCW) with a wide range of densities along a near critical isotherm using the simple point charge extended (SPC/E) pair potential in order to study the entropy and the solvation shell structure around a central water molecule. It is shown that both the translational and orientational two-particle correlation entropy terms can serve as the metrics of the translational-orientational structural orders in water and it is revealed that the translational structural order is very sensitive to the density variation in the gas-like and liquid-like region, while the orientational structural order is much more dependent upon compression in the medium-density SCW region. The comparison of the magnitudes of the full thermodynamic excess entropy and two-particle correlation entropy confirms the recent findings that the many-body terms other than two-body ones also present significant and non-neglectable contributions to the full excess entropy for the highly anomalous fluids like water. The analysis of entropy terms as a function of intermolecular distance and the orientational distribution functions as well as the three-dimensional spatial distribution functions indicate that the structural order occurs only in a much more diffused first solvation shell due to the elongated hydrogen bonds under supercritical conditions. It is revealed that no obvious second or higher neighbor shells occur in SCW, in contrast with the feature of normal liquid water that the anomalous decrease of translational order upon compression occurs mainly in the second shell.

  17. Molecular dynamics simulations of peptides at the air-water interface: influencing factors on peptide-templated mineralization.

    Science.gov (United States)

    Jain, Alok; Jochum, Mara; Peter, Christine

    2014-12-30

    Biomineralization is the intricate, biomedically highly relevant process by which living organisms deposit minerals on biological matrices to stiffen tissues and build skeletal structures and shells. Rapaport and coworkers ( J. Am. Chem. Soc. 2000 , 122 , 12523 ; Adv. Funct. Mater. 2008 , 18 , 2889 ; Acta Biomater. 2012 , 8 , 2466 ) have designed a class of self-assembling amphiphilic peptides that are capable of forming hydrogels and attracting ions from the environment, generating structures akin to the extracellular matrix and promoting bone regeneration. The air-water interface serves both in experiment and in simulations as a model hydrophobic surface to mimic the cell's organic-aqueous interface and to investigate the organization of the peptide matrix into ordered β-pleated monolayers and the subsequent onset of biomineral formation. To obtain insight into the underlying molecular mechanism, we have used molecular dynamics simulations to study the effect of peptide sequence on aggregate stability and ion-peptide interactions. We find-in excellent agreement with experimental observations-that the nature of the peptide termini (proline vs phenylalanine) affect the aggregate order, while the nature of the acidic side chains (aspartic vs glutamic acid) affect the aggregate's stability in the presence of ions. These simulations provide valuable microscopic insight into the way ions and peptide templates mutually affect each other during the early stages of biomineralization preceding nucleation.

  18. Evaporation of water droplets on Pt-surface in presence of external electric field--A molecular dynamics study.

    Science.gov (United States)

    Hens, Abhiram; Biswas, Gautam; De, Sudipta

    2015-09-01

    Evaporation of a sessile droplet on a hot solid substrate is an important problem in fluid mechanics. It is relevant to theoretical issues in heat transfer as well as several practical applications. This study investigates the spreading and evaporation of a nanoscale water droplet on a solid platinum surface. The major objective was to analyze the effect of an external electric field on these phenomena. Varying the intensity and direction of the external electric field, a series of molecular dynamics simulations were carried out to understand these phenomena at a molecular level. The results reveal that a horizontal electric field assists in droplet spreading, whereas a vertical electric field enhances the rate of evaporation for a certain range of field intensities. It also shows that the substrate temperature plays an important role in such processes. It is seen that the effect of an external electric field on droplet evaporation becomes significant at an intermediate range of surface temperatures and this effect is not clearly visible for either very high or very low range of surface temperatures.

  19. Revealing Surface Waters on an Antifreeze Protein by Fusion Protein Crystallography Combined with Molecular Dynamic Simulations.

    Science.gov (United States)

    Sun, Tianjun; Gauthier, Sherry Y; Campbell, Robert L; Davies, Peter L

    2015-10-01

    Antifreeze proteins (AFPs) adsorb to ice through an extensive, flat, relatively hydrophobic surface. It has been suggested that this ice-binding site (IBS) organizes surface waters into an ice-like clathrate arrangement that matches and fuses to the quasi-liquid layer on the ice surface. On cooling, these waters join the ice lattice and freeze the AFP to its ligand. Evidence for the generality of this binding mechanism is limited because AFPs tend to crystallize with their IBS as a preferred protein-protein contact surface, which displaces some bound waters. Type III AFP is a 7 kDa globular protein with an IBS made up two adjacent surfaces. In the crystal structure of the most active isoform (QAE1), the part of the IBS that docks to the primary prism plane of ice is partially exposed to solvent and has clathrate waters present that match this plane of ice. The adjacent IBS, which matches the pyramidal plane of ice, is involved in protein-protein crystal contacts with few surface waters. Here we have changed the protein-protein contacts in the ice-binding region by crystallizing a fusion of QAE1 to maltose-binding protein. In this 1.9 Å structure, the IBS that fits the pyramidal plane of ice is exposed to solvent. By combining crystallography data with MD simulations, the surface waters on both sides of the IBS were revealed and match well with the target ice planes. The waters on the pyramidal plane IBS were loosely constrained, which might explain why other isoforms of type III AFP that lack the prism plane IBS are less active than QAE1. The AFP fusion crystallization method can potentially be used to force the exposure to solvent of the IBS on other AFPs to reveal the locations of key surface waters.

  20. All-Atom Continuous Constant pH Molecular Dynamics With Particle Mesh Ewald and Titratable Water.

    Science.gov (United States)

    Huang, Yandong; Chen, Wei; Wallace, Jason A; Shen, Jana

    2016-11-08

    Development of a pH stat to properly control solution pH in biomolecular simulations has been a long-standing goal in the community. Toward this goal recent years have witnessed the emergence of the so-called constant pH molecular dynamics methods. However, the accuracy and generality of these methods have been hampered by the use of implicit-solvent models or truncation-based electrostatic schemes. Here we report the implementation of the particle mesh Ewald (PME) scheme into the all-atom continuous constant pH molecular dynamics (CpHMD) method, enabling CpHMD to be performed with a standard MD engine at a fractional added computational cost. We demonstrate the performance using pH replica-exchange CpHMD simulations with titratable water for a stringent test set of proteins, HP36, BBL, HEWL, and SNase. With the sampling time of 10 ns per replica, most pKa's are converged, yielding the average absolute and root-mean-square deviations of 0.61 and 0.77, respectively, from experiment. Linear regression of the calculated vs experimental pKa shifts gives a correlation coefficient of 0.79, a slope of 1, and an intercept near 0. Analysis reveals inadequate sampling of structure relaxation accompanying a protonation-state switch as a major source of the remaining errors, which are reduced as simulation prolongs. These data suggest PME-based CpHMD can be used as a general tool for pH-controlled simulations of macromolecular systems in various environments, enabling atomic insights into pH-dependent phenomena involving not only soluble proteins but also transmembrane proteins, nucleic acids, surfactants, and polysaccharides.

  1. Structural Properties of Liquid Water and Ice Ih from Ab-Initio Molecular Dynamics with a Non-Local Correlation Functional

    Directory of Open Access Journals (Sweden)

    Niall J. English

    2015-08-01

    Full Text Available Equilibrium Born-Oppenheimer molecular dynamics simulations have been performed in the canonical ensemble to investigate the structural properties of liquid water and ice Ih (hexagonal ice at 298 and 273 K, respectively, using a state-of-the-art non-local correlation functional, whilst size effects have been examined explicitly in the case of liquid water. This has led to improved agreement with experiments for pair distribution functions, in addition to molecular dipole moments, vis-à-vis previous flavours of ab-initio molecular dynamics simulation of water, highlighting the importance of appropriate dispersion. Intramolecular geometry has also been examined, in addition to hydrogen-bonding interactions; it was found that an improved description of dispersion via non-local correlation helps to reduce over-structuring associated with the Perdew-Becke-Ernzerhof (PBE and other commonly-used functionals.

  2. Molecular dynamics studies of simple membrane-water interfaces: Structure and functions in the beginnings of cellular life

    Science.gov (United States)

    Pohorille, Andrew; Wilson, Michael A.

    1995-01-01

    Molecular dynamics computer simulations of the structure and functions of a simple membrane are performed in order to examine whether membranes provide an environment capable of promoting protobiological evolution. Our model membrane is composed of glycerol 1-monooleate. It is found that the bilayer surface fluctuates in time and space, occasionally creating thinning defects in the membrane. These defects are essential for passive transport of simple ions across membranes because they reduce the Born barrier to this process by approximately 40%. Negative ions are transferred across the bilayer more readily than positive ions due to favorable interactions with the electric field at the membrane-water interface. Passive transport of neutral molecules is, in general, more complex than predicted by the solubility-diffusion model. In particular, molecules which exhibit sufficient hydrophilicity and lipophilicity concentrate near membrane surfaces and experience 'interfacial resistance' to transport. The membrane-water interface forms an environment suitable for heterogeneous catalysis. Several possible mechanisms leading to an increase of reaction rates at the interface are discussed. We conclude that vesicles have many properties that make them very good candidates for earliest protocells. Some potentially fruitful directions of experimental and theoretical research on this subject are proposed.

  3. Molecular dynamics studies of simple membrane-water interfaces: Structure and functions in the beginnings of cellular life

    Science.gov (United States)

    Pohorille, Andrew; Wilson, Michael A.

    1995-01-01

    Molecular dynamics computer simulations of the structure and functions of a simple membrane are performed in order to examine whether membranes provide an environment capable of promoting protobiological evolution. Our model membrane is composed of glycerol 1-monooleate. It is found that the bilayer surface fluctuates in time and space, occasionally creating thinning defects in the membrane. These defects are essential for passive transport of simple ions across membranes because they reduce the Born barrier to this process by approximately 40%. Negative ions are transferred across the bilayer more readily than positive ions due to favorable interactions with the electric field at the membrane-water interface. Passive transport of neutral molecules is, in general, more complex than predicted by the solubility-diffusion model. In particular, molecules which exhibit sufficient hydrophilicity and lipophilicity concentrate near membrane surfaces and experience 'interfacial resistance' to transport. The membrane-water interface forms an environment suitable for heterogeneous catalysis. Several possible mechanisms leading to an increase of reaction rates at the interface are discussed. We conclude that vesicles have many properties that make them very good candidates for earliest protocells. Some potentially fruitful directions of experimental and theoretical research on this subject are proposed.

  4. Nuclear Quantum Effects in Liquid Water: A Highly Accurate ab initio Path-Integral Molecular Dynamics Study

    Science.gov (United States)

    Distasio, Robert A., Jr.; Santra, Biswajit; Ko, Hsin-Yu; Car, Roberto

    2014-03-01

    In this work, we report highly accurate ab initio path-integral molecular dynamics (AI-PIMD) simulations on liquid water at ambient conditions utilizing the recently developed PBE0+vdW(SC) exchange-correlation functional, which accounts for exact exchange and a self-consistent pairwise treatment of van der Waals (vdW) or dispersion interactions, combined with nuclear quantum effects (via the colored-noise generalized Langevin equation). The importance of each of these effects in the theoretical prediction of the structure of liquid water will be demonstrated by a detailed comparative analysis of the predicted and experimental oxygen-oxygen (O-O), oxygen-hydrogen (O-H), and hydrogen-hydrogen (H-H) radial distribution functions as well as other structural properties. In addition, we will discuss the theoretically obtained proton momentum distribution, computed using the recently developed Feynman path formulation, in light of the experimental deep inelastic neutron scattering (DINS) measurements. DOE: DE-SC0008626, DOE: DE-SC0005180.

  5. Interactive molecular dynamics

    CERN Document Server

    Schroeder, Daniel V

    2015-01-01

    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.

  6. Interactive molecular dynamics

    Science.gov (United States)

    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.

  7. From Molecular Dynamics to Brownian Dynamics

    CERN Document Server

    Erban, Radek

    2014-01-01

    Three coarse-grained molecular dynamics (MD) models are investigated with the aim of developing and analyzing multiscale 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.

  8. Molecular mechanism of polymer-assisting supersaturation of poorly water-soluble loratadine based on experimental observations and molecular dynamic simulations.

    Science.gov (United States)

    Zhang, Shenwu; Sun, Mengchi; Zhao, Yongshan; Song, Xuyang; He, Zhonggui; Wang, Jian; Sun, Jin

    2017-07-05

    Polymers have been usually used to retard nucleation and crystal growth in order to maintain supersaturation, yet their roles in inhibition of nucleation and crystal growth are poorly understood. In our work, the polymer-based supersaturation performances and molecular mechanisms of poorly aqueous soluble loratadine were investigated. Two common hydrophilic polymers (hydroxylpropylmethyl cellulose acetate succinate (HPMC-AS) and poly(vinylpyrrolidone-co-vinyl-acetate) (PVP-VA)) were used. It was found that HPMC-AS was a better polymer to prevent drug molecules from aggregation and to maintain the supersaturated state in solution than PVP-VA. The in vitro dissolution experiments showed that HPMC-AS solid dispersions had more rapid release at pH 4.5 and 6.8 media than PVP-VA solid dispersions under the un-sink condition. Moreover, molecular dynamic simulation results showed that HPMC-AS was more firmly absorbed onto a surface of the drug nanoparticles than PVP-VA due to bigger hydrophobic areas of HPMC-AS. Thereby, crystallization process of loratadine was inhibited in the presence of water to provide prolonged stability of the supersaturated state. In conclusion, polymers played a key role in maintaining supersaturation state of loratadine solid dispersions by strong drug-polymer interactions and the hydrophobic characteristic of polymers.

  9. Influence of gravity on the collective molecular dynamics of liquid water: the case of the floating water bridge

    CERN Document Server

    Del Giudice, Emilio

    2010-01-01

    Quantum electrodynamics (QED) produces a picture of liquid water as a mixture of a low density coherent phase and an high density non-coherent phase. Consequently, the Archimedes principle prescribes that, within a gravitational field, liquid water should be made up, at surface, mainly of the coherent fraction, which becomes a cage where the gas-like non-coherent fraction is trapped, acquiring a non-vanishing pressure (vapor tension). Therefore, it is possible to probe the QED picture by observing the behavior of liquid water under reduced gravity conditions. The floating water bridge could be a useful test model.

  10. Solvatochromic shift of phenol blue in water from a combined Car-Parrinello molecular dynamics hybrid quantum mechanics-molecular mechanics and ZINDO approach

    Science.gov (United States)

    Murugan, N. Arul; Jha, Prakash Chandra; Rinkevicius, Z.; Ruud, Kenneth; Ågren, Hans

    2010-06-01

    The present work addresses the solvatochromic shift of phenol blue (PB) dye. For this purpose the results of Car-Parrinello molecular dynamics (CPMD) simulations for PB in gas phase are compared with results obtained for PB in water from CPMD hybrid quantum mechanics-molecular mechanics (CPMD-QM/MM) calculations. The absorption spectra were obtained using the intermediate neglect of differential overlap/spectroscopic-configuration interaction (INDO/CIS) method and were calculated for a multitude of configurations of the trajectory. The calculated λmax for PB in gas phase was found to be about 535 nm, which is considerably lower than the λmax reported for PB in nonpolar solvents. Different solvation shells for PB in water have been defined based on the solute-all-atoms and solvent center of mass radial distribution function (g(rX-O)). The electronic excitation energies for PB computed in the presence of solvent molecules in an increasing number of solvation shells were calculated in a systematic way to evaluate their contributions to the solvatochrmic shift. The inclusion of solvent molecules in the hydration shell yields a λmax of 640 nm, which contributes to almost 78% of the solvatochromic shift. The inclusion of solvent molecules up to 10 Å in the g(rX-O) rdf yields a λmax of 670 nm which is in good agreement with the experimentally reported value of 654-684 nm. Overall, the present study suggests that the combined CPMD-QM/MM and INDO-CIS approach can be used successfully to model solvatochromic shifts of organic dye molecules.

  11. A polarizable model of water for molecular dynamics simulations of biomolecules

    Science.gov (United States)

    Lamoureux, Guillaume; Harder, Edward; Vorobyov, Igor V.; Roux, Benoît; MacKerell, Alexander D.

    2006-01-01

    The SWM4-DP polarizable water model [G. Lamoureux, A.D. MacKerell, Jr., B. Roux, J. Chem. Phys. 119 (2003) 5185], based on classical Drude oscillators, is re-optimized for negatively charged Drude particles. The new model, called SWM4-NDP, will be incorporated into a polarizable biomolecular force field currently in development. It is calibrated to reproduce important properties of the neat liquid at room temperature and pressure: vaporization enthalpy, density, static dielectric constant and self-diffusion constant. In this Letter, we also show that it yields the correct liquid shear viscosity and free energy of hydration.

  12. Modeling the Hydrogen Bond within Molecular Dynamics

    Science.gov (United States)

    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.

  13. Molecular Dynamics Calculations

    Science.gov (United States)

    1996-01-01

    The development of thermodynamics and statistical mechanics is very important in the history of physics, and it underlines the difficulty in dealing with systems involving many bodies, even if those bodies are identical. Macroscopic systems of atoms typically contain so many particles that it would be virtually impossible to follow the behavior of all of the particles involved. Therefore, the behavior of a complete system can only be described or predicted in statistical ways. Under a grant to the NASA Lewis Research Center, scientists at the Case Western Reserve University have been examining the use of modern computing techniques that may be able to investigate and find the behavior of complete systems that have a large number of particles by tracking each particle individually. This is the study of molecular dynamics. In contrast to Monte Carlo techniques, which incorporate uncertainty from the outset, molecular dynamics calculations are fully deterministic. Although it is still impossible to track, even on high-speed computers, each particle in a system of a trillion trillion particles, it has been found that such systems can be well simulated by calculating the trajectories of a few thousand particles. Modern computers and efficient computing strategies have been used to calculate the behavior of a few physical systems and are now being employed to study important problems such as supersonic flows in the laboratory and in space. In particular, an animated video (available in mpeg format--4.4 MB) was produced by Dr. M.J. Woo, now a National Research Council fellow at Lewis, and the G-VIS laboratory at Lewis. This video shows the behavior of supersonic shocks produced by pistons in enclosed cylinders by following exactly the behavior of thousands of particles. The major assumptions made were that the particles involved were hard spheres and that all collisions with the walls and with other particles were fully elastic. The animated video was voted one of two

  14. Potential of hydrogen bond in water. Comparison of the theory with vibrational spectra and results of molecular dynamics simulations.

    Science.gov (United States)

    Efimov, Yuri Ya; Naberukhin, Yuri I

    2011-02-01

    Potential of hydrogen bond is the function which relates its energy to geometrical parameters of hydrogen bridge: its length R(O…O) and angles between direction O…O and OH group [φ (H-O…O)] and/or lone pair of proton accepting oxygen atom [χ(-O…O)]. Previously we have suggested an approach to design such potentials based on the approximate numerical solution of a reverse problem of the spectrum band shape in the frames of the fluctuation theory of hydrogen bonding. In the given work this method is applied to construction of the two-parameter potentials that depend on parameters {R(O…O), φ (H-O…O} or {φ (H-O…O), χ (-O…O)}. Using them, the spectra of OH vibrations of HOD molecules in a liquid phase are calculated theoretically in good agreement with experiment in the temperature range up to 200 °C. Distributions of angles P(φ, T), P(χ, T), and energies P(E) are calculated also. The same distributions and spectra are independently calculated on the basis of the geometrical parameters of the hydrogen bridges obtained from molecular dynamics models of water. The shapes of the spectral contours and their temperature evolution calculated for computer models turned out to be similar to experimental ones only for the potential that includes the length of H-bond R(O…O).

  15. Dynamic characteristic of amitriptyline in water by ultrasonic relaxation method and molecular orbital calculation.

    Science.gov (United States)

    Nishikawa, Sadakatsu; Kamimura, Eri

    2011-02-03

    Ultrasonic absorption coefficients in the frequency range of 0.8-220 MHz have been measured in aqueous solution of amitriptyline (3-(10,11-dihydro-5H-dibenzo[a,d]cycloheptene-5-ylidene)-N,N-dimethyl-1-propanamine) in the concentration range from 0.20 to 0.60 mol dm(-3) at 25 °C. A single relaxational phenomenon has been observed, and the relaxation frequency is independent of the concentration. It has been also observed that the amplitude of the relaxational absorption increases linearly with the analytical concentration. From these ultrasonic relaxation data, it has been concluded that the relaxation is associated with a unimolecular reaction due to a conformational change of the solute molecule, such as a structural change due to a rotational motion of a group in the solute molecule. Molecular orbital semiempirical methods using AM1 (Austin model 1) and PM3 (modified neglect of diatomic overlap parametric method 3) have been applied to obtain the standard enthalpy of formation for amitriptyline molecule at various dihedral angles around one of the bonds in alkylamine side chain. The results have shown the two clear minimum standard enthalpies of formation for amitriptyline. From the difference of the two values, the standard enthalpy change between the two stable conformers has been calculated be 2.9 kJ mol(-1). On a rough assumption that the standard enthalpy change reflects the standard free energy change, the equilibrium constant for the rotational isomers has been estimated to be 0.31. Combining this value with the experimental ultrasonic relaxation frequency, the backward and forward rate constants have been evaluated. The standard enthalpy change of the reaction has been also estimated from the concentration dependence of the maximum absorption per wavelength, and it has been close to that calculated by the semiempirical methods. The ultrasonic absorption measurements have been also carried out in amitriptyline solution in the presence of

  16. Generation and integration of NaOH into NaCl clusters in supercritical water: a molecular dynamics study on hydrolysis product partitioning.

    Science.gov (United States)

    Nahtigal, Istok G; Svishchev, Igor M

    2009-11-05

    The interaction of water with NaCl nanoparticles at supercritical conditions has been studied by molecular dynamics (MD) simulation. During the nanoparticle nucleation process, water is not only physically adsorbed to the periphery of the NaCl cluster but also exists in a confined state within subsurface regions for several picoseconds. Electrostatic fields generated by the coalescing ions are shown to be on the order of 10(10) V/m, which can drive the hydrolysis of confined water molecules. A molecular mechanism for the sodium chloride hydrolysis reaction at supercritical conditions is suggested. It involves proton transfer from water to chloride ions, followed by hydrolysis product partitioning. We provide MD results displaying the subsurface hydroxide localization in amorphous NaCl clusters, as well as the partitioning of the HCl into the supercritical water phase.

  17. Molecular dynamics simulations of the tribological behaviour of a water-lubricated amorphous carbon-fluorine PECVD coating

    Science.gov (United States)

    Rullich, Markus; Weiss, Volker C.; Frauenheim, Thomas

    2013-07-01

    Hybrid bearings comprising ceramic balls and steel rings exhibit increased wear-resistance and a reduced coefficient of friction (COF) compared with standard steel bearings. Using plasma-enhanced chemical vapour deposition (PECVD) coatings to modify the surface properties, the performance of these bearings can be further improved. Fluorine-containing amorphous hydrogenated carbon (a-C : F : H) films are well suited to this purpose. To study the influence of such coatings on the friction characteristics of key parts of hybrid bearings, a model of an a-C : F : H film was constructed and employed in molecular dynamics simulations of two slabs sliding past each other, lubricated by water. With one slab being pulled by a virtual spring, the perpendicular force (load) was kept constant using a barostat. For comparison, a system of two silicon dioxide (cristobalite) slabs and a mixed system consisting of a cristobalite slab and an a-C : F : H slab were investigated. Our results indicate a linear dependence of the friction force on the perpendicular force. With an increasing amount of water between the slabs, the COFs decrease. A decrease in temperature leads to an increased COF, while a decrease in the relative velocity of the slabs does not influence the COF between two a-C : F : H slabs, but reduces the COF for the other two systems. Our results for the COF and its dependence on temperature and relative sliding velocity generally agree well both with experiments and with simulations for similar systems reported in the literature.

  18. Density dependence of hydrogen bonding and the translational-orientational structural order in supercritical water: a molecular dynamics study.

    Science.gov (United States)

    Ma, Haibo; Ma, Jing

    2011-08-07

    Molecular dynamics simulation have been performed with a wide range of densities along a near critical isotherm of supercritical water (SCW) in order to study the density dependence of the structure order and hydrogen bonding (HB). It is revealed that the translational structure order is nearly invariant while the orientational tetrahedral structure order is very sensitive to the bulk density under supercritical conditions. Meanwhile, some energetically unfavorable intermediate water dimer structures are found to appear under supercritical conditions due to the reduced energy difference and the enhanced energy fluctuation. As a consequence, a general geometrical criterion or the inclusion of a energy-based criterion instead of currently widely adopted pure r(OH)-based geometric criterion is suggested to be used in the HB statistics under supercritical conditions. It is found that the average HB number per H(2)O molecule (n(HB)) reduces with the decreasing SCW bulk density although a given pair of H(2)O molecules are shown to have a stronger ability to form a hydrogen bond under lower SCW bulk densities. Accordingly, the orientational tetrahedral structure order q decreases with the reducing bulk density under supercritical conditions. However, when the fluid is dilute with ρ ≤ 0.19ρ(c) (ρ(c) = 0.322 g/cm(3)), the energy fluctuation increases sharply and the short-range order is destroyed, signifying the supercritical fluid (SCF)-gas state transition. Accordingly, the orientational tetrahedral structure order q gets reversal around ρ = 0.19ρ(c) and approaches zero under very dilute conditions. The sensitivity of the orientational order to the density implies the microscopic origin of the significant dependence of SCF's physicochemical properties on the pressure.

  19. Molecular Dynamics and Protein Function

    National Research Council Canada - National Science Library

    M. Karplus; J. Kuriyan; Bruce J. Berne

    2005-01-01

    .... Molecular dynamics simulations provide powerful tools for the exploration of the conformational energy landscape accessible to these molecules, and the rapid increase in computational power coupled...

  20. Molecular dynamics analysis of the friction between a water-methanol liquid mixture and a non-polar solid crystal surface

    Science.gov (United States)

    Nakaoka, Satoshi; Yamaguchi, Yasutaka; Omori, Takeshi; Joly, Laurent

    2017-05-01

    We performed molecular dynamics analysis of the momentum transfer at the solid-liquid interface for a water-methanol liquid mixture between parallel non-polar solid walls in order to understand the strong decrease of the friction coefficient (FC) induced by the methanol adsorption at the surface observed in our previous work [S. Nakaoka et al., Phys. Rev. E 92, 022402 (2015)]. In particular, we extracted the individual contributions of water and methanol molecules to the total FC and found that the molecular FC for methanol was larger than that for water. We further showed that the reduction of the total solid-liquid FC upon the increase of the methanol molar fraction in the first adsorption layer occurred as a result of a decrease in the molecular number density as well as a decrease in the molecular FCs of both molecules. Analysis of the molecular orientation revealed that the decrease of the molecular FC of methanol resulted from changes of the contact feature onto the solid surface. Specifically, methanol molecules near the solid surface had their C-O bond parallel to the surface with both CH3 and O sites contacting the solid at low methanol molar fraction, while they had their C-O bond outward from the surface with only the CH3 site contacting the solid at higher methanol molar fraction. The mechanisms discussed in this work could be used to search for alternative water additives to further reduce the solid-liquid friction.

  1. Investigation of the structure of ethanol-water mixtures by molecular dynamics simulation I: analyses concerning the hydrogen-bonded pairs.

    Science.gov (United States)

    Gereben, Orsolya; Pusztai, László

    2015-02-19

    Series of molecular dynamics simulations for ethanol-water mixtures with 20-80 mol % ethanol content, pure ethanol, and water were performed. In each mixture, for ethanol the OPLS force field was used, combined with three different water force fields, the SPC/E, the TIP4P-2005, and the SWM4-DP. Water potential models were distinguished on the basis of deviations between calculated and measured total scattering X-ray structure factors aided by ethanol-water pair binding energy comparison. No single water force field could provide the best agreement with experimental data at all concentrations: at the ethanol content of 80% the SWM-DP, for 60 mol % the SWM4-DP and the TIP4P-2005, whereas for the 40 and 20 mol % mixtures TIP4P-2005 water force field provided the closest match. Coordination numbers and hydrogen bonds/molecule values were calculated, revealing that the oxygen-oxygen first coordination numbers strongly overestimate the average number of hydrogen bonds/molecule. The center-of-molecule distributions indicate that the ethanol-ethanol first coordination sphere expands with increasing water concentration while the size of the first water-water coordination sphere does not change. Various two and three-dimensional distributions were calculated that reveal the differences between simulations with different water force fields. Detailed conformational analyses of the hydrogen-bonded pairs were performed; drawings of the characteristic molecular arrangements are provided.

  2. Molecular Dynamics of Lipid Bilayers

    Science.gov (United States)

    1989-08-09

    The aim of this work is to study, by molecular dynamics simulations, the properties of lipid bilayers. We have applied the vectorizable, order-N...fast angle-dependent force/potential algorithms to treat angle bending and torsion. Keywords: Molecular dynamics , Lipid bilayers.

  3. Structure, interfacial properties, and dynamics of the sodium alkyl sulfate type surfactant monolayer at the water/trichloroethylene interface: a molecular dynamics simulation study.

    Science.gov (United States)

    Shi, Wen-Xiong; Guo, Hong-Xia

    2010-05-20

    In this work, we perform a series of molecular dynamics (MD) simulations on the category of sodium alkyl sulfate (SDS-type) surfactant monolayers at the water/trichloroethylene (TCE) interface. Three separate tail-length SDS-type molecules are used. We investigate the conformation of surfactant chain (i.e., packing, orientation, and order), interfacial properties (i.e., interfacial thickness, interfacial tension, area compressibility, and bending modulus), their dependence on the chain length, and the average area per surfactant chain. We also examine the behavior of the surfactant monolayer in the metastable regime of negative surface tension with reference to collapse. The simulation has clearly shown that the very dilute monolayer is well described as a two-dimensional gas. With the increase of interfacial surfactant coverage, the monolayer is in the liquid-expanded (LE) phase. The surfactant tails at the interface become straighter, more ordered, and thicker at higher surfactant coverage. At the same time, interfacial tension of long-tail systems is always lower than that of short-tail systems. In the LE phase, the area compressibility modulus and the bending modulus increase with an increase in tail length. With a further decrease in molecular areas, the monolayer with large negative surface tension becomes unstable. Our simulations show that buckling of the monolayers is of dynamic nature as a response to mechanical instability. The further transformation pathway from buckling to bud can be controlled by the bending modulus, which depends crucially on the tail length and interfacial surfactant coverage. At a given area per molecule, the short tail chain makes the monolayer softer, and the budding process becomes more probable. For the supersaturated softer SDS monolayer, the collapse transition is initiated by the buckling of monolayers, followed primarily by budding and detachment of the nanoscale swollen micelle from the monolayer. Despite a number of

  4. Potentials of mean force for the exo and endo solvolysis of 2-norbornyl chloride in water and DMSO: A constrained molecular dynamics study

    Indian Academy of Sciences (India)

    Subodh C Tiwari; Timir Hajari; Ashish Sharma; B L Tembe

    2012-01-01

    Constrained molecular dynamics is used to calculate the potentials of mean force for the exo and endo dissociation of 2-norbornyl chlorides in two solvents, namely water and dimethyl sulphoxide (DMSO). The gas phase potential energy curves for the 2-norbornyl chlorides are computed by ab initio methods and these curves are fitted into a 12-6-1 potential for use in classical molecular dynamics simulations. The gas phase potential energy curves indicate a greater barrier for the dissociation of the endo 2-norbornyl chloride (than the exo). The potentials of mean force (PMF) in DMSO and water indicate the locations and the magnitudes of the activation barriers in these solutions and are sensitive functions of the fitted gas phase potentials.

  5. MDplot: Visualise Molecular Dynamics.

    Science.gov (United States)

    Margreitter, Christian; Oostenbrink, Chris

    2017-05-10

    The MDplot package provides plotting functions to allow for automated visualisation of molecular dynamics simulation output. It is especially useful in cases where the plot generation is rather tedious due to complex file formats or when a large number of plots are generated. The graphs that are supported range from those which are standard, such as RMsD/RMsF (root-mean-square deviation and root-mean-square fluctuation, respectively) to less standard, such as thermodynamic integration analysis and hydrogen bond monitoring over time. All told, they address many commonly used analyses. In this article, we set out the MDplot package's functions, give examples of the function calls, and show the associated plots. Plotting and data parsing is separated in all cases, i.e. the respective functions can be used independently. Thus, data manipulation and the integration of additional file formats is fairly easy. Currently, the loading functions support GROMOS, GROMACS, and AMBER file formats. Moreover, we also provide a Bash interface that allows simple embedding of MDplot into Bash scripts as the final analysis step. The package can be obtained in the latest major version from CRAN (https://cran.r-project.org/package=MDplot) or in the most recent version from the project's GitHub page at https://github.com/MDplot/MDplot, where feedback is also most welcome. MDplot is published under the GPL-3 license.

  6. Efficient "on-the-fly" calculation of Raman spectra from \\textit{ab-initio} molecular dynamics: Application to hydrophobic/hydrophilic solutes in bulk water

    CERN Document Server

    Partovi-Azar, Pouya

    2015-01-01

    We present a computational method to accurately calculate Raman spectra from first principles with an at least one order of magnitude higher efficiency. This scheme thus allows to routinely calculate finite-temperature Raman spectra "on-the-fly" by means of \\textit{ab-initio} molecular dynamics simulations. To demonstrate the predictive power of this approach we investigate the effect of hydrophobic and hydrophilic solutes in water solution on the infrared and Raman spectra.

  7. Temperature-dependent solubilities and mean ionic activity coefficients of alkali halides in water from molecular dynamics simulations

    Science.gov (United States)

    Mester, Zoltan; Panagiotopoulos, Athanassios Z.

    2015-07-01

    The mean ionic activity coefficients of aqueous KCl, NaF, NaI, and NaCl solutions of varying concentrations have been obtained from molecular dynamics simulations following a recently developed methodology based on gradual insertions of salt molecules [Z. Mester and A. Z. Panagiotopoulos, J. Chem. Phys. 142, 044507 (2015)]. The non-polarizable ion models of Weerasinghe and Smith [J. Chem. Phys. 119, 11342 (2003)], Gee et al. [J. Chem. Theory Comput. 7, 1369 (2011)], Reiser et al. [J. Chem. Phys. 140, 044504 (2014)], and Joung and Cheatham [J. Phys. Chem. B 112, 9020 (2008)] were used along with the extended simple point charge (SPC/E) water model [Berendsen et al., J. Phys. Chem. 91, 6269 (1987)] in the simulations. In addition to the chemical potentials in solution used to obtain the activity coefficients, we also calculated the chemical potentials of salt crystals and used them to obtain the solubility of these alkali halide models in SPC/E water. The models of Weerasinghe and Smith [J. Chem. Phys. 119, 11342 (2003)] and Gee et al. [J. Chem. Theory Comput. 7, 1369 (2011)] provide excellent predictions of the mean ionic activity coefficients at 298.15 K and 1 bar, but significantly underpredict or overpredict the solubilities. The other two models generally predicted the mean ionic activity coefficients only qualitatively. With the exception of NaF for which the solubility is significantly overpredicted, the model of Joung and Cheatham predicts salt solubilities that are approximately 40%-60% of the experimental values. The models of Reiser et al. [J. Chem. Phys. 140, 044504 (2014)] make good predictions for the NaCl and NaI solubilities, but significantly underpredict the solubilities for KCl and NaF. We also tested the transferability of the models to temperatures much higher than were used to parametrize them by performing simulations for NaCl at 373.15 K and 1 bar, and at 473.15 K and 15.5 bar. All models overpredict the drop in the values of mean ionic

  8. Path Integral Molecular Dynamics within the Grand Canonical-like Adaptive Resolution Technique: Quantum-Classical Simulation of Liquid Water

    CERN Document Server

    Agarwal, Animesh

    2015-01-01

    Quantum effects due to the spatial delocalization of light atoms are treated in molecular simulation via the path integral technique. Among several methods, Path Integral (PI) Molecular Dynamics (MD) is nowadays a powerful tool to investigate properties induced by spatial delocalization of atoms; however computationally this technique is very demanding. The abovementioned limitation implies the restriction of PIMD applications to relatively small systems and short time scales. One possible solution to overcome size and time limitation is to introduce PIMD algorithms into the Adaptive Resolution Simulation Scheme (AdResS). AdResS requires a relatively small region treated at path integral level and embeds it into a large molecular reservoir consisting of generic spherical coarse grained molecules. It was previously shown that the realization of the idea above, at a simple level, produced reasonable results for toy systems or simple/test systems like liquid parahydrogen. Encouraged by previous results, in this ...

  9. Aggregation behaviors of PEO-PPO-ph-PPO-PEO and PPO-PEO-ph-PEO-PPO at an air/water interface: experimental study and molecular dynamics simulation.

    Science.gov (United States)

    Gong, Houjian; Xu, Guiying; Liu, Teng; Xu, Long; Zhai, Xueru; Zhang, Jian; Lv, Xin

    2012-09-25

    The block polyethers PEO-PPO-ph-PPO-PEO (BPE) and PPO-PEO-ph-PEO-PPO (BEP) are synthesized by anionic polymerization using bisphenol A as initiator. Compared with Pluronic P123, the aggregation behaviors of BPE and BEP at an air/water interface are investigated by the surface tension and dilational viscoelasticity. The molecular construction can influence the efficiency and effectiveness of block polyethers in decreasing surface tension. BPE has the most efficient ability to decrease surface tension of water among the three block polyethers. The maximum surface excess concentration (Γ(max)) of BPE is larger than that of BEP or P123. Moreover, the dilational modulus of BPE is almost the same as that of P123, but much larger than that of BEP. The molecular dynamics simulation provides the conformational variations of block polyethers at the air/water interface.

  10. Activated carbon immersed in water-the origin of linear correlation between enthalpy of immersion and oxygen content studied by molecular dynamics simulation.

    Science.gov (United States)

    Terzyk, Artur P; Gauden, Piotr A; Furmaniak, Sylwester; Wesołowski, Radosław P; Kowalczyk, Piotr

    2010-09-28

    First Molecular Dynamics simulation results of activated carbon immersion in water are reported. Using a Virtual Porous Carbon Model of "soft" carbon the influence of surface oxygen content, distribution of groups and micropore diameter on the enthalpy of immersion is studied. The empirical relation between enthalpy and concentration of surface groups (as well as polar surface area) is reproduced by molecular simulation results. It is shown that for strongly hydrophobic carbons immersed in water, the water-vapour interface inside pores appears. This interface vanishes with the rise in content of surface oxygen. We discuss some nuances of the interfacial region using proximal distribution functions and hydrogen bonds statistics. Finally we conclude that the mechanism of immersion process is in accordance with Pratt-Chandler theory of hydrophobic interactions.

  11. Nonequilibrium molecular dynamics simulations of the thermal conductivity of water: a systematic investigation of the SPC/E and TIP4P/2005 models.

    Science.gov (United States)

    Römer, Frank; Lervik, Anders; Bresme, Fernando

    2012-08-21

    We report an extensive nonequilibrium molecular dynamics investigation of the thermal conductivity of water using two of the most accurate rigid nonpolarizable empirical models available, SPC/E and TIP4P/2005. Our study covers liquid and supercritical states. Both models predict the anomalous increase of the thermal conductivity with temperature and the thermal conductivity maximum, hence confirming their ability to reproduce the complex anomalous behaviour of water. The performance of the models strongly depends on the thermodynamic state investigated, and best agreement with experiment is obtained for states close to the liquid coexistence line and at high densities and temperatures. Considering the simplicity of these two models the overall agreement with experiments is remarkable. Our results show that explicit polarizability and molecular flexibility are not needed to reproduce the anomalous heat conduction of water.

  12. Effect of Adsorbed Alcohol Layers on the Behavior of Water Molecules Confined in a Graphene Nanoslit: A Molecular Dynamics Study.

    Science.gov (United States)

    Gao, Qingwei; Zhu, Yudan; Ruan, Yang; Zhang, Yumeng; Zhu, Wei; Lu, Xiaohua; Lu, Linghong

    2017-09-11

    With the rapid development of a two-dimensional (2D) nanomaterial, the confined liquid binary mixture has attracted increasing attention, which has significant potential in membrane separation. Alcohol/water is one of the most common systems in liquid-liquid separation. As one of the most focused systems, recent studies have found that ethanol molecules were preferentially adsorbed on the inner surface of the pore wall and formed an adsorbed ethanol layer under 2D nanoconfinement. To evaluate the effect of the alcohol adsorption layer on the mobility of water molecules, molecular simulations were performed to investigate four types of alcohol/water binary mixtures confined under a 20 Å graphene slit. Residence times of the water molecules covering the alcohol layer were in the order of methanol/water molecules and the surrounding water molecules could induce a small degree of damage to the H-bond network of the water molecules covering the alcohol layer, resulting in the long residence time of the water molecules.

  13. Prototropic tautomerism of 4-Methyl 1,2,4-Triazole-3-Thione molecule in solvent water medium: DFT and Car-Parrinello molecular dynamics study

    Science.gov (United States)

    Dutta, Bipan; De, Rina; Chowdhury, Joydeep

    2015-12-01

    The ground state prototropic tautomerism of 4-Methyl 1,2,4-Triazole-3-Thione molecule in solvent water medium has been investigated with the aid of DFT and Car-Parrinello molecular dynamics (CPMD) simulation studies. The CPMD simulations envisage the possibility of proton transfer reactions of the molecule through the solvent water medium. Probable proton transfer pathways have been predicted from the DFT calculations which are substantiated by the natural bond orbital analyses. The evolution and breaking of the concerned bonds of the molecule for different proton transfer reaction pathways are also estimated.

  14. A charge-driven molecular water pump

    Science.gov (United States)

    Gong, Xiaojing; Li, Jingyuan; Lu, Hangjun; Wan, Rongzheng; Li, Jichen; Hu, Jun; Fang, Haiping

    2007-11-01

    Understanding and controlling the transport of water across nanochannels is of great importance for designing novel molecular devices, machines and sensors and has wide applications, including the desalination of seawater. Nanopumps driven by electric or magnetic fields can transport ions and magnetic quanta, but water is charge-neutral and has no magnetic moment. On the basis of molecular dynamics simulations, we propose a design for a molecular water pump. The design uses a combination of charges positioned adjacent to a nanopore and is inspired by the structure of channels in the cellular membrane that conduct water in and out of the cell (aquaporins). The remarkable pumping ability is attributed to the charge dipole-induced ordering of water confined in the nanochannels, where water can be easily driven by external fields in a concerted fashion. These findings may provide possibilities for developing water transport devices that function without osmotic pressure or a hydrostatic pressure gradient.

  15. Temperature dependence of protein hydration hydrodynamics by molecular dynamics simulations.

    Energy Technology Data Exchange (ETDEWEB)

    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.

  16. Study of clathrate hydrates via equilibrium molecular-dynamics simulation employing polarisable and non-polarisable, rigid and flexible water models

    Science.gov (United States)

    Burnham, Christian J.; English, Niall J.

    2016-04-01

    Equilibrium molecular-dynamics (MD) simulations have been performed on metastable sI and sII polymorphs of empty hydrate lattices, in addition to liquid water and ice Ih. The non-polarisable TIP4P-2005, simple point charge model (SPC), and polarisable Thole-type models (TTM): TTM2, TTM3, and TTM4 water models were used in order to survey the differences between models and to see what differences can be expected when polarisability is incorporated. Rigid and flexible variants were used of each model to gauge the effects of flexibility. Power spectra are calculated and compared to density-of-states spectra inferred from inelastic neutron scattering (INS) measurements. Thermodynamic properties were also calculated, as well as molecular-dipole distributions. It was concluded that TTM models offer optimal fidelity vis-à-vis INS spectra, together with thermodynamic properties, with the flexible TTM2 model offering optimal placement of vibrational modes.

  17. Molecular dynamics of silicon indentation

    Energy Technology Data Exchange (ETDEWEB)

    Kallman, J.S.; Hoover, W.G.; Hoover, C.G.; De Groot, A.J.; Lee, S.M.; Wooten, F. (Department of Applied Science Davis-Livermore, Lawrence Livermore National Laboratory, Livermore, California 94550 (United States))

    1993-04-01

    We use nonequilibrium molecular dynamics to simulate the elastic-plastic deformation of silicon under tetrahedral nanometer-sized indentors. The results are described in terms of a rate-dependent and temperature-dependent phenomenological yield strength. We follow the structural change during indentation with a computer technique that allows us to model the dynamic simulation of diffraction patterns.

  18. TES buffer-induced phase separation of aqueous solutions of several water-miscible organic solvents at 298.15 K: phase diagrams and molecular dynamic simulations.

    Science.gov (United States)

    Taha, Mohamed; Lee, Ming-Jer

    2013-06-28

    Water and the organic solvents tetrahydrofuran, 1,3-dioxolane, 1,4-dioxane, 1-propanol, 2-propanol, tert-butanol, acetonitrile, or acetone are completely miscible in all proportions at room temperature. Here, we present new buffering-out phase separation systems that the above mentioned organic aqueous solutions can be induced to form two liquid phases in the presence of a biological buffer 2-[[1,3-dihydroxy-2-(hydroxymethyl)propan-2-yl]amino]ethanesulfonic acid (TES). The lower liquid phase is rich in water and buffer, and the upper phase is organic rich. This observation has both practical and mechanistic interests. The phase diagrams of these systems were constructed by experimental measurements at ambient conditions. Molecular dynamic (MD) simulations were performed for TES + water + THF system to understand the interactions between TES, water, and organic solvent at molecular level. Several composition-sets for this system, beyond and inside the liquid-liquid phase-splitting region, have been simulated. Interestingly, the MD simulation for compositions inside the phase separation region showed that THF molecules are forced out from the water network to start forming a new liquid phase. The hydrogen-bonds, hydrogen-bonds lifetimes, hydrogen-bond energies, radial distribution functions, coordination numbers, the electrostatic interactions, and the van der Waals interactions between the different pairs have been calculated. Additionally, MD simulations for TES + water + tert-butanol∕acetonitrile∕acetone phase separation systems were simulated. The results from MD simulations provide an explanation for the buffering-out phenomena observed in [TES + water + organic solvent] systems by a mechanism controlled by the competitive interactions of the buffer and the organic solvent with water. The molecular mechanism reported here is helpful for designing new benign separation materials.

  19. Cotransporters as molecular water pumps

    DEFF Research Database (Denmark)

    Zeuthen, Thomas; MacAulay, Nanna

    2002-01-01

    Molecular water pumps are membrane proteins of the cotransport type in which a flux of water is coupled to substrate fluxes by a mechanism within the protein. Free energy can be exchanged between the fluxes. Accordingly, the flux of water may be relatively independent of the external water chemical...

  20. Molecular modelling and molecular dynamics of CFTR.

    Science.gov (United States)

    Callebaut, Isabelle; Hoffmann, Brice; Lehn, Pierre; Mornon, Jean-Paul

    2017-01-01

    The cystic fibrosis transmembrane conductance regulator (CFTR) protein is a member of the ATP-binding cassette (ABC) transporter superfamily that functions as an ATP-gated channel. Considerable progress has been made over the last years in the understanding of the molecular basis of the CFTR functions, as well as dysfunctions causing the common genetic disease cystic fibrosis (CF). This review provides a global overview of the theoretical studies that have been performed so far, especially molecular modelling and molecular dynamics (MD) simulations. A special emphasis is placed on the CFTR-specific evolution of an ABC transporter framework towards a channel function, as well as on the understanding of the effects of disease-causing mutations and their specific modulation. This in silico work should help structure-based drug discovery and design, with a view to develop CFTR-specific pharmacotherapeutic approaches for the treatment of CF in the context of precision medicine.

  1. Molecular dynamic simulations of ocular tablet dissolution.

    Science.gov (United States)

    Ru, Qian; Fadda, Hala M; Li, Chung; Paul, Daniel; Khaw, Peng T; Brocchini, Steve; Zloh, Mire

    2013-11-25

    Small tablets for implantation into the subconjunctival space in the eye are being developed to inhibit scarring after glaucoma filtration surgery (GFS). There is a need to evaluate drug dissolution at the molecular level to determine how the chemical structure of the active may correlate with dissolution in the nonsink conditions of the conjunctival space. We conducted molecular dynamics simulations to study the dissolution process of tablets derived from two drugs that can inhibit fibrosis after GFS, 5-fluorouracil (5-FU) and the matrix metalloprotease inhibitor (MMPi), ilomastat. The dissolution was simulated in the presence of simple point charge (SPC) water molecules, and the liquid turnover of the aqueous humor in the subconjunctival space was simulated by removal of the dissolved drug molecules at regular intervals and replacement by new water molecules. At the end of the simulation, the total molecular solvent accessible surface area of 5-FU tablets increased by 60 times more than that of ilomastat as a result of tablet swelling and release of molecules into solution. The tablet dissolution pattern shown in our molecular dynamic simulations tends to correlate with experimental release profiles. This work indicates that a series of molecular dynamic simulations can be used to predict the influence of the molecular properties of a drug on its dissolution profile and could be useful during preformulation where sufficient amounts of the drug are not always available to perform dissolution studies.

  2. Chemical Theory and Computation Special Feature: Static and dynamic quantum effects in molecular liquids: A linearized path integral description of water

    Science.gov (United States)

    Aage Poulsen, Jens; Nyman, Gunnar; Rossky, Peter J.

    2005-05-01

    Structure, transport properties, and IR spectra including quantum effects are calculated for a flexible simple point charge model of liquid water. A recently introduced combination of a variational local harmonic description of the liquid potential surface and the classical Wigner approximation for the dynamics is used. The potential energy and interatomic radial distribution functions are in good agreement with accurate results from the literature and are significantly closer to experiment than predictions found from classical theory. The oxygen and hydrogen velocity correlation functions are also calculated, and the corresponding molecular diffusion coefficient is in good accord with existing theoretical estimates including quantum effects. Of most interest, an ab initio quantum correction factor is obtained to correct the far IR spectrum of water. When corrected, a spectrum based on a classical simulation yields results that agree well with experiment. Combined with internal tests of consistency, these observations indicate that this quite flexible approach will be effective for a variety of molecular problems involving the dynamics of light nuclei. computer simulation | liquid dynamics

  3. Is dynamic heterogeneity of water in presence of a protein denaturing agent different from that in presence of a protein stabilizer? A molecular dynamics simulation study

    Indian Academy of Sciences (India)

    SANDIPA INDRA; RANJIT BISWAS BISWAS

    2016-12-01

    Rotational and translational dynamic heterogeneities (DHs) of ambient aqueous solutions of trimethylamine-N-oxide (TMAO) and tetramethylurea (TMU) at several solute concentrations have been investigated and compared. Motional characteristics of water molecules at solute interfaces and in bulk solutionshave been thoroughly examined for the search of slow dynamics. Note, TMAO possesses zwitterionic structure and is a protein stabilizer whereas TMU is a neutral dipolar molecule and a strong denaturant. Results suggest that water-TMAO solutions possess stronger DH than water-TMU solutions with the solute concentration dependence being stronger for TMAO than for TMU. Diffusive dynamics slows down near the solute surface for both the solutes. Solvation structure shows TMAO-water interaction is stronger than TMU-waterinteraction, producing longer H-bond fluctuation timescale in TMAO solutions. In short, this paper presents, for the first time, a systematic and comparative study of motional features and inter-species interactions between aqueous solutions containing solutes that differ in their individual impacts on protein stability.

  4. Multiscale Reactive Molecular Dynamics

    Science.gov (United States)

    2012-08-15

    as a linear combination of several possible bond- ing topologies ( diabatic states) that are coupled to one an- other through the off-diagonal elements...adapts and dynamically identifies bonding topolo- gies to include as the simulation progresses. These bonding topologies form a basis of diabatic ...the original geometric factor. The diabatic correction term, VCORR , used here was labeled in previous MS-EVB models as a repulsive interaction, VREP

  5. State-Dependent Molecular Dynamics

    Directory of Open Access Journals (Sweden)

    Ciann-Dong Yang

    2014-10-01

    Full Text Available 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.

  6. Molecular dynamics simulation of pyridine

    Science.gov (United States)

    Trumpakaj, Zygmunt; Linde, Bogumił

    2015-04-01

    Molecular Dynamics (MD) simulations are used for the investigation of molecular motions in pyridine in the temperature range 20-480 K under normal pressure. The results obtained are analyzed within the frame of the Mori Zwanzig memory function formalism. An analytical approximation of the first memory function K(t) is applied to predict some dependences on temperature. Experimental results of the Rayleigh scattering of depolarized light from liquid pyridine are used as the main base for the comparison.

  7. Uranyl ion interaction at the water/NiO(100) interface: A predictive investigation by first-principles molecular dynamic simulations

    Energy Technology Data Exchange (ETDEWEB)

    Sebbari, Karim [EDF-R and D, Departement Materiaux et Mecanique des Composants, Les Renardieres, Ecuelles, 77818 Moret Sur Loing (France); Institut de Physique Nucleaire d' Orsay, Universite Paris-Sud, CNRS UMR 8608, 15 rue Georges Clemenceau, Batiment 100, 91406 Orsay Cedex (France); Roques, Jerome; Simoni, Eric [Institut de Physique Nucleaire d' Orsay, Universite Paris-Sud, CNRS UMR 8608, 15 rue Georges Clemenceau, Batiment 100, 91406 Orsay Cedex (France); Domain, Christophe [EDF-R and D, Departement Materiaux et Mecanique des Composants, Les Renardieres, Ecuelles, 77818 Moret Sur Loing (France)

    2012-10-28

    The behavior of the UO{sub 2}{sup 2+} uranyl ion at the water/NiO(100) interface was investigated for the first time using Born-Oppenheimer molecular dynamic simulations with the spin polarized DFT +U extension. A water/NiO(100) interface model was first optimized on a defect-free five layers slab thickness, proposed as a reliable surface model, with an explicit treatment of the solvent. Water molecules are adsorbed with a well-defined structure in a thickness of about 4 A above the surface. The first layer, adsorbed on nickel atoms, remains mainly in molecular form but can partly dissociate at 293 K. Considering low acidic conditions, a bidentate uranyl ion complex was characterized on two surface oxygen species (arising from water molecules adsorption on nickel atoms) with d{sub U-O{sub a{sub d{sub s{sub o{sub r{sub p{sub t{sub i{sub o{sub n}}}}}}}}}}}=2.39 A. This complex is stable at 293 K due to iono-covalent bonds with an estimated charge transfer of 0.58 electron from the surface to the uranyl ion.

  8. Uranyl ion interaction at the water/NiO(100) interface: a predictive investigation by first-principles molecular dynamic simulations.

    Science.gov (United States)

    Sebbari, Karim; Roques, Jérôme; Domain, Christophe; Simoni, Eric

    2012-10-28

    The behavior of the UO(2)(2+) uranyl ion at the water/NiO(100) interface was investigated for the first time using Born-Oppenheimer molecular dynamic simulations with the spin polarized DFT + U extension. A water/NiO(100) interface model was first optimized on a defect-free five layers slab thickness, proposed as a reliable surface model, with an explicit treatment of the solvent. Water molecules are adsorbed with a well-defined structure in a thickness of about 4 Å above the surface. The first layer, adsorbed on nickel atoms, remains mainly in molecular form but can partly dissociate at 293 K. Considering low acidic conditions, a bidentate uranyl ion complex was characterized on two surface oxygen species (arising from water molecules adsorption on nickel atoms) with d(U-O(adsorption))=2.39 Å. This complex is stable at 293 K due to iono-covalent bonds with an estimated charge transfer of 0.58 electron from the surface to the uranyl ion.

  9. Water O-H bond activation by gas-phase plutonium atoms: reaction mechanisms and ab initio molecular dynamics study.

    Science.gov (United States)

    Li, Peng; Niu, Wenxia; Gao, Tao; Wang, Hongyan

    2014-10-06

    A thorough description of the reaction mechanisms, taking into account different possible spin states, offers insights into the gas-phase reaction of plutonium atoms with water. Two possible reactions (isomerization and dehydrogenation) are presented. These reactions are found to be exothermic, with the best thermochemical conditions observed for the dehydrogenation reaction at around 23.5 kcal mol(-1). The nature of the chemical-bonding evolution along the reaction pathways are investigated by employing various methods including electron localization function, atoms in molecules, and Mayer bond order. Total, partial, and overlap population density of state diagrams and analyses are also presented. Reaction rates at elevated temperatures (T=298-2 000 K) are calculated by using variational transition-state theory with one-dimensional tunneling effects. In dynamics simulations, only the dehydrogenation reaction is observed, and found to be in good agreement with experimental values.

  10. Wettability behavior of water droplet on organic-polluted fused quartz surfaces of pillar-type nanostructures applying molecular dynamics simulation

    Science.gov (United States)

    Chen, Jiaxuan; Chen, Wenyang; Xie, Yajing; Wang, Zhiguo; Qin, Jianbo

    2017-02-01

    Molecular dynamics (MD) is applied to research the wettability behaviors of different scale of water clusters absorbed on organic-polluted fused quartz (FQ) surface and different surface structures. The wettability of water clusters is studied under the effect of organic pollutant. With the combined influence of pillar height and interval, the stair-step Wenzel-Cassie transition critical line is obtained by analyzing stable state of water clusters on different surface structures. The results also show that when interval of pillars and the height of pillars keep constant respectively, the changing rules are exactly the opposite and these are termed as the "waterfall" rules. The substrate models of water clusters at Cassie-Baxter state which are at the vicinity of critical line are chosen to analyze the relationship of HI (refers to the pillar height/interval) ratio and scale of water cluster. The study has found that there is a critical changing threshold in the wettability changing process. When the HI ratio keeps constant, the wettability decreases first and then increase as the size of cluster increases; on the contrary, when the size of cluster keeps constant, the wettability decreases and then increase with the decrease of HI ratio, but when the size of water cluster is close to the threshold the HI ratio has little effect on the wettability.

  11. Characteristics of hydration water around hen egg lysozyme as the protein model in aqueous solution. FTIR spectroscopy and molecular dynamics simulation.

    Science.gov (United States)

    Panuszko, Aneta; Wojciechowski, Marek; Bruździak, Piotr; Rakowska, Paulina W; Stangret, Janusz

    2012-12-05

    In this paper, the hydration of a model protein--hen egg white lysozyme in aqueous solution has been presented. The leading method used was FTIR spectroscopy with an application of a technique of semi-heavy water (HDO) isotope dilution. Analysis of spectra of HDO isotopically diluted in water solution of lysozyme allowed us to isolate HDO spectra affected by lysozyme, and thus to characterise the energetic state of water molecules and their arrangement around protein molecules. The number of water molecules and the shape of the affected HDO spectrum were obtained using a classical and a chemometric method. This shape showed that the HDO spectrum affected by lysozyme may be presented as a superposition of two spectra corresponding to HDO affected by N-methylacetamide and the carboxylate anion (of the formic acid). Moreover, based on the difference in intermolecular distances distribution of water molecules (obtained from spectral data), we demonstrated that the lysozyme molecule causes a decrease in population of weak hydrogen bonds, and concurrently increases the probability of an occurrence of short hydrogen bonds in water affected by lysozyme. This conclusion was also confirmed by the molecular dynamics (MD) simulation.

  12. Dynamic molecular graphs: "hopping" structures.

    Science.gov (United States)

    Cortés-Guzmán, Fernando; Rocha-Rinza, Tomas; Guevara-Vela, José Manuel; Cuevas, Gabriel; Gómez, Rosa María

    2014-05-05

    This work aims to contribute to the discussion about the suitability of bond paths and bond-critical points as indicators of chemical bonding defined within the theoretical framework of the quantum theory of atoms in molecules. For this purpose, we consider the temporal evolution of the molecular structure of [Fe{C(CH2 )3 }(CO)3 ] throughout Born-Oppenheimer molecular dynamics (BOMD), which illustrates the changing behaviour of the molecular graph (MG) of an electronic system. Several MGs with significant lifespans are observed across the BOMD simulations. The bond paths between the trimethylenemethane and the metallic core are uninterruptedly formed and broken. This situation is reminiscent of a "hopping" ligand over the iron atom. The molecular graph wherein the bonding between trimethylenemethane and the iron atom takes place only by means of the tertiary carbon atom has the longest lifespan of all the considered structures, which is consistent with the MG found by X-ray diffraction experiments and quantum chemical calculations. In contrast, the η(4) complex predicted by molecular-orbital theory has an extremely brief lifetime. The lifespan of different molecular structures is related to bond descriptors on the basis of the topology of the electron density such as the ellipticities at the FeCH2 bond-critical points and electron delocalisation indices. This work also proposes the concept of a dynamic molecular graph composed of the different structures found throughout the BOMD trajectories in analogy to a resonance hybrid of Lewis structures. It is our hope that the notion of dynamic molecular graphs will prove useful in the discussion of electronic systems, in particular for those in which analysis on the basis of static structures leads to controversial conclusions. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  13. Optical dynamics of molecular aggregates

    NARCIS (Netherlands)

    de Boer, Steven

    2006-01-01

    The subject of this thesis is the spectroscopy and dynamics of molecular aggregates in amorphous matrices. Aggregates of three different molecules were studied. The molecules are depicted in Fig. (1.1). Supersaturated solutions of these molecules show aggregate formation. Aggregation is a process si

  14. Temperature dependence of the microscopic structure and density anomaly of the SPC/E and TIP4P-Ew water models. Molecular dynamics simulation results

    Directory of Open Access Journals (Sweden)

    E. Galicia-Andrés

    2015-03-01

    Full Text Available We have investigated temperature trends of the microscopic structure of the SPC/E and TIP4P-Ew water models in terms of the pair distribution functions, coordination numbers, the average number of hydrogen bonds, the distribution of bonding states of a single molecule as well as the angular distribution of molecules by using the constant pressure molecular dynamics simulations. The evolution of the structure is put in correspondence with the dependence of water density on high temperatures down to the region of temperatures where the system becomes supercooled. It is shown that the fraction of molecules with three and four bonds determine the maximum density for both models. Moreover, the temperature dependence of the dielectric constant is obtained and analyzed.

  15. Phase transition study of confined water molecules inside carbon nanotubes: hierarchical multiscale method from molecular dynamics simulation to ab initio calculation.

    Science.gov (United States)

    Javadian, Soheila; Taghavi, Fariba; Yari, Faramarz; Hashemianzadeh, Seyed Majid

    2012-09-01

    In this study, the mechanism of the temperature-dependent phase transition of confined water inside a (9,9) single-walled carbon nanotube (SWCNT) was studied using the hierarchical multi-scale modeling techniques of molecular dynamics (MD) and density functional theory (DFT). The MD calculations verify the formation of hexagonal ice nanotubes at the phase transition temperature T(c)=275K by a sharp change in the location of the oxygen atoms inside the SWCNT. Natural bond orbital (NBO) analysis provides evidence of considerable intermolecular charge transfer during the phase transition and verifies that the ice nanotube contains two different forms of hydrogen bonding due to confinement. Nuclear quadrupole resonance (NQR) and nuclear magnetic resonance (NMR) analyses were used to demonstrate the fundamental influence of intermolecular hydrogen bonding interactions on the formation and electronic structure of ice nanotubes. In addition, the NQR analysis revealed that the rearrangement of nano-confined water molecules during the phase transition could be detected directly by the orientation of ¹⁷O atom EFG tensor components related to the molecular frame axes. The effects of nanoscale confinements in ice nanotubes and water clusters were analyzed by experimentally observable NMR and NQR parameters. These findings showed a close relationship between the phase behavior and orientation of the electronic structure in nanoscale structures and demonstrate the usefulness of NBO and NQR parameters for detecting phase transition phenomena in nanoscale confining environments.

  16. The accurate calculation of the band gap of liquid water by means of GW corrections applied to plane-wave density functional theory molecular dynamics simulations.

    Science.gov (United States)

    Fang, Changming; Li, Wun-Fan; Koster, Rik S; Klimeš, Jiří; van Blaaderen, Alfons; van Huis, Marijn A

    2015-01-07

    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.

  17. Molecular dynamics simulation of the processive endocellulase Cel48F from Clostridium cellulolyticum: a novel "water-control mechanism" in enzymatic hydrolysis of cellulose.

    Science.gov (United States)

    Zhang, Hao; Zhang, Ji-long; Sun, Lu; Niu, Xiao-di; Wang, Song; Shan, Ya-ming

    2014-07-01

    Glycoside hydrolase of Cel48F from Clostridium cellulolyticum is an important processive cellulose, which can hydrolyze cellulose into cellobiose. Molecular dynamics simulations were used to investigate the hydrolysis mechanism of cellulose. The two conformations of the Cel48F-cellotetrose complex in which the cellotetroses are bound at different sites (known as the sliding conformation and the hydrolyzing conformation) were simulated. By comparing these two conformations, a water-control mechanism is proposed, in which the hydrolysis proceeds by providing a water molecule for every other glucosidic linkage. The roles of certain key residues are determined: Glu55 and Asp230 are the most probable candidates for acid and base, respectively, in the mechanism of inverting anomeric carbon. Met414 and Trp417 constitute the water-control system. Glu44 might keep the substrate at a certain location within the active site or help the substrate chain to move from the sliding conformation to the hydrolyzing conformation. The other hydrophobic residues around the substrate can decrease the sliding energy barrier or provide a hydrophobic environment to resist entry of the surrounding water molecules into the active site, except for those coming from a specific water channel. Copyright © 2014 John Wiley & Sons, Ltd.

  18. Deprotonation states of the two active site water molecules regulate the binding of protein phosphatase 5 with its substrate: a molecular dynamics study.

    Science.gov (United States)

    Wang, Lingyun; Yan, Feng

    2017-07-20

    Protein phosphatase 5 (PP5), mainly localized in human brain, can dephosphorylate tau protein whose high level of phosphorylation is related to Alzheimer's disease. Similar to other protein phosphatases, PP5 has a conserved motif in the catalytic domain that contains two binding sites for manganese (Mn(2+) ) ions. Structural data indicate that two active site water molecules, one bridging the two Mn(2+) ions and the other terminally coordinated with one of the Mn(2+) ions (Mn1), are involved in catalysis. Recently, a density functional theory study revealed that the two water molecules can be both deprotonated to keep a neutral active site for catalysis. The theoretical study gives us an insight into the catalytic mechanism of PP5, but the knowledge of how the deprotonation states of the two water molecules affect the binding of PP5 with its substrate is still lacking. To approach this problem, molecular dynamics simulations were performed to model the four possible deprotonation states. Through structural, dynamical and energetic analyses, the results demonstrate that the deprotonation states of the two water molecules affect the structure of the active site including the distance between the two Mn(2+) ions and their coordination, impact the interaction energy of residues R275, R400 and H304 which directly interact with the substrate phosphoserine, and mediate the dynamics of helix αJ which is involved in regulation of the enzyme's activity. Furthermore, the deprotonation state that is preferable for PP5 binding of its substrate has been identified. These findings could provide new design strategy for PP5 inhibitor. © 2017 The Protein Society.

  19. Probing the wild-type HRas activation mechanism using steered molecular dynamics, understanding the energy barrier and role of water in the activation.

    Science.gov (United States)

    Sharma, Neeru; Sonavane, Uddhavesh; Joshi, Rajendra

    2014-03-01

    Ras is one of the most common oncogenes in human cancers. It belongs to a family of GTPases that functions as binary conformational switches by timely switching of their conformations from GDP to GTP and vice versa. It attains the final active state structure via an intermediate GTP-bound state. The transition between these states is a millisecond-time-scale event. This makes studying this mechanism beyond the scope of classical molecular dynamics. In the present study, we describe the activation pathway of the HRas protein complex along the distance-based reaction coordinate using steered molecular dynamics. Approximately ~720 ns of MD simulations using CMD and SMD was performed. We demonstrated the change in orientation and arrangement of the two switch regions and the role of various hydrogen bonds during the activation process. The weighted histogram analysis method was also performed, and the potential of mean force was calculated between the inactive and active via the intermediate state (state 1) of HRas. The study indicates that water seems to play a crucial role in the activation process and to transfer the HRas protein from its intermediate state to the fully active state. The implications of our study hereby suggest that the HRas activation mechanism is a multistep process. It starts from the inactive state to an intermediate state 1 followed by trapping of water molecules and flipping of the Thr35 residue to form a fully active state (state 2). This state 2 also comprises Gly60, Thr35, GTP, Mg(2+) and water-forming stable interactions.

  20. Escape of water molecular from Carbon Nanotubes

    Science.gov (United States)

    Li, Jiaxi; Li, Wenfeng; Zhang, Jianwei

    2014-03-01

    Understanding and controlling the transport of water molecules through nanopores have attracted great interest due to potential applications for designing novel nanofluidic devices, machines and sensors. In this work, we theoretically investigate the effects of an external nonuniform electric field on the escape of water molecules through single-walled carbon nanotubes (SWNTs) by using of molecular dynamics (MD) simulations. When polar water molecules are placed in the gradient electric field, the electric force is experienced that can drive the water molecules. Molecular dynamics simulations show that the escape probability of water obeys the Boltzmann distribution. Our results show that energy barrier delta E is independent of temperature which indicates that it is a single-barrier system. From the MD results statistics, the key parameters could be determined such that the relationship between energy barrier delta E and diameter of SWNTs and nozzle distance of the charge r would be revealed that could deepen our current theoretical understanding on transport of water molecular inside SWNTs with the nonuniform electric field.

  1. The [BMI][Tf2N] ionic liquid/water binary system: a molecular dynamics study of phase separation and of the liquid-liquid interface.

    Science.gov (United States)

    Sieffert, N; Wipff, G

    2006-07-01

    We report molecular dynamics (MD) simulations of the aqueous interface of the hydrophobic [BMI][Tf2N] ionic liquid (IL), composed of 1-butyl-3-methylimidazolium cations (BMI+) and bis(trifluoromethylsulfonyl)imide anions (Tf2N-). The questions of water/IL phase separation and properties of the neat interface are addressed, comparing different liquid models (TIP3P vs TIP5P water and +1.0/-1.0 vs +0.9/-0.9 charged IL ions), the Ewald vs the reaction field treatments of the long range electrostatics, and different starting conditions. With the different models, the "randomly" mixed liquids separate much more slowly (in 20 to 40 ns) than classical water-oil mixtures do (typically, in less than 1 ns), finally leading to distinct nanoscopic phases separated by an interface, as in simulations which started with a preformed interface, but the IL phase is more humid. The final state of water in the IL thus depends on the protocol and relates to IL heterogeneities and viscosity. Water mainly fluctuates in hydrophilic basins (rich in O(Tf2N) and aromatic CH(BMI) groups), separated by more hydrophobic domains (rich in CF3(Tf2N) and alkyl(BMI) groups), in the form of monomers and dimers in the weakly humid IL phase, and as higher aggregates when the IL phase is more humid. There is more water in the IL than IL in water, to different extents, depending on the model. The interface is sharper and narrower (approximately 10 A) than with the less hydrophobic [BMI][PF6] IL and is overall neutral, with isotropically oriented molecules, as in the bulk phases. The results allow us to better understand the analogies and differences of aqueous interfaces with hydrophobic (but hygroscopic) ILs, compared to classical organic liquids.

  2. Development of a group contribution method for estimating free energy of peptides in a dodecane-water system via molecular dynamic simulations.

    Science.gov (United States)

    Mora Osorio, Camilo Andrés; González Barrios, Andrés Fernando

    2016-12-07

    Calculation of the Gibbs free energy changes of biological molecules at the oil-water interface is commonly performed with Molecular Dynamics simulations (MD). It is a process that could be performed repeatedly in order to find some molecules of high stability in this medium. Here, an alternative method of calculation has been proposed: a group contribution method (GCM) for peptides based on MD of the twenty classic amino acids to obtain free energy change during the insertion of any peptide chain in water-dodecane interfaces. Multiple MD of the twenty classic amino acids located at the interface of rectangular simulation boxes with a dodecane-water medium were performed. A GCM to calculate the free energy of entire peptides is then proposed. The method uses the summation of the Gibbs free energy of each amino acid adjusted in function of its presence or absence in the chain as well as its hydrophobic characteristics. Validation of the equation was performed with twenty-one peptides all simulated using MD in dodecane-water rectangular boxes in previous work, obtaining an average relative error of 16%.

  3. Thermal Conductivity of Ordered Molecular Water

    Energy Technology Data Exchange (ETDEWEB)

    W Evans; J Fish; P Keblinski

    2006-02-16

    We use molecular dynamics simulation to investigate thermal transport characteristics of water with various degree of orientational and translational order induced by the application of an electric field. We observe that orientational ordering of the water dipole moments has a minor effect on the thermal conductivity. However, electric-field induced crystallization and associated translational order results in approximately a 3-fold increase of thermal conductivity with respect to the base water, i.e., to values comparable with those characterizing ice crystal structures.

  4. Available Instruments for Analyzing Molecular Dynamics Trajectories.

    Science.gov (United States)

    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.

  5. Dynamical Non-Equilibrium Molecular Dynamics

    Directory of Open Access Journals (Sweden)

    Giovanni Ciccotti

    2013-12-01

    Full Text Available In this review, we discuss the Dynamical approach to Non-Equilibrium Molecular Dynamics (D-NEMD, which extends stationary NEMD to time-dependent situations, be they responses or relaxations. Based on the original Onsager regression hypothesis, implemented in the nineteen-seventies by Ciccotti, Jacucci and MacDonald, the approach permits one to separate the problem of dynamical evolution from the problem of sampling the initial condition. D-NEMD provides the theoretical framework to compute time-dependent macroscopic dynamical behaviors by averaging on a large sample of non-equilibrium trajectories starting from an ensemble of initial conditions generated from a suitable (equilibrium or non-equilibrium distribution at time zero. We also discuss how to generate a large class of initial distributions. The same approach applies also to the calculation of the rate constants of activated processes. The range of problems treatable by this method is illustrated by discussing applications to a few key hydrodynamic processes (the “classical” flow under shear, the formation of convective cells and the relaxation of an interface between two immiscible liquids.

  6. Feynman-Kleinert Linearized Path Integral (FK-LPI) Algorithms for Quantum Molecular Dynamics, with Application to Water and He(4).

    Science.gov (United States)

    Poulsen, Jens Aage; Nyman, Gunnar; Rossky, Peter J

    2006-11-01

    The Feynman-Kleinert Linearized Path Integral (FK-LPI) representation of quantum correlation functions is extended in applications and algorithms. Diffusion including quantum effects for a flexible simple point charge model of liquid water is explored, including new tests of internal consistency. An ab initio quantum correction factor (QCF) is also obtained to correct the far-infrared spectrum of water. After correction, a spectrum based on a classical simulation is in good agreement with the experiment. The FK-LPI QCF is shown to be superior to the so-called harmonic QCF. New computational algorithms are introduced so that the quantum Boltzmann Wigner phase-space density, the central object in the implementation, can be obtained for arbitrary potentials. One scheme requires only that the standard classical force routine be replaced when turning from one molecular problem to another. The new algorithms are applied to the calculation of the Van Hove spectrum of liquid He(4) at 27 K. The spectrum moments are in very good agreement with the experiment. These observations indicate that the FK-LPI approach can be broadly effective for molecular problems involving the dynamics of light nuclei.

  7. Reactive molecular dynamics models from ab initio molecular dynamics data using relative entropy minimization

    Science.gov (United States)

    Arntsen, Christopher; Chen, Chen; Voth, Gregory A.

    2017-09-01

    We present two new multiscale molecular dynamics (MS-RMD) models for the hydrated excess proton in water developed directly from ab initio molecular dynamics (AIMD) simulation data of the same system. The potential of mean force along the proton transfer reaction coordinate and radial distribution functions for the MS-RMD models are shown to faithfully reproduce those of AIMD. The models are developed using an algorithm based on relative entropy minimization, thus demonstrating the ability of the method to rapidly generate accurate and highly efficient reactive MD force fields.

  8. An Evaluation of the Scattering Law for Light and Heavy Water in ENDF-6 Format, Based on Experimental Data and Molecular Dynamics

    Science.gov (United States)

    Márquez Damián, J. I.; Granada, J. R.; Malaspina, D. C.

    2014-04-01

    In this work we present an evaluation in ENDF-6 format of the scattering law for light and heavy water computed using the LEAPR module of NJOY99. The models used in this evaluation are based on experimental data on light water dynamics measured by Novikov, partial structure factors obtained by Soper, and molecular dynamics calculations performed with GROMACS using a reparameterized version of the flexible SPC model by Toukan and Rahman. The models use the Egelstaff-Schofield diffusion equation for translational motion, and a continuous spectrum calculated from the velocity autocorrelation function computed with GROMACS. The scattering law for H in H2O is computed using the incoherent approximation, and the scattering law D and O in D2O are computed using the Sköld approximation for coherent scattering. The calculations show significant improvement over ENDF/B-VI and ENDF/B-VII when compared with measurements of the total cross section, differential scattering experiments and quasi-elastic neutron scattering experiments (QENS).

  9. Molecular Dynamics for Dense Matter

    CERN Document Server

    Maruyama, Toshiki; Chiba, Satoshi

    2012-01-01

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

  10. Phase-transfer energetics of small-molecule alcohols across the water-hexane interface: molecular dynamics simulations using charge equilibration models.

    Science.gov (United States)

    Bauer, Brad A; Zhong, Yang; Meninger, David J; Davis, Joseph E; Patel, Sandeep

    2011-04-01

    We study the water-hexane interface using molecular dynamics (MD) and polarizable charge equilibration (CHEQ) force fields. Bulk densities for TIP4P-FQ water and hexane, 1.0086±0.0002 and 0.6378±0.0001 g/cm(3), demonstrate excellent agreement with experiment. Interfacial width and interfacial tension are consistent with previously reported values. The in-plane component of the dielectric permittivity (ɛ(||)) for water is shown to decrease from 81.7±0.04 to unity, transitioning longitudinally from bulk water to bulk hexane. ɛ(||) for hexane reaches a maximum in the interface, but this term represents only a small contribution to the total dielectric constant (as expected for a non-polar species). Structurally, net orientations of the molecules arise in the interfacial region such that hexane lies slightly parallel to the interface and water reorients to maximize hydrogen bonding. Interfacial potentials due to contributions of the water and hexane are calculated to be -567.9±0.13 and 198.7±0.01 mV, respectively, giving rise to a total potential in agreement with the range of values reported from previous simulations of similar systems. Potentials of mean force (PMF) calculated for methanol, ethanol, and 1-propanol for the transfer from water to hexane indicate an interfacial free energy minimum, corresponding to the amphiphilic nature of the molecules. The magnitudes of transfer free energies were further characterized from the solvation free energies of alcohols in water and hexane using thermodynamic integration. This analysis shows that solvation free energies for alcohols in hexane are 0.2-0.3 kcal/mol too unfavorable, whereas solvation of alcohols in water is approximately 1 kcal/mol too favorable. For the pure hexane-water interfacial simulations, we observe a monotonic decrease of the water dipole moment to near-vacuum values. This suggests that the electrostatic component of the desolvation free energy is not as severe for polarizable models than for

  11. Hydrogen bonding and induced dipole moments in water: predictions from the Gaussian charge polarizable model and Car-Parrinello molecular dynamics.

    Science.gov (United States)

    Dyer, Peter J; Cummings, Peter T

    2006-10-14

    We compare a new classical water model, which features Gaussian charges and polarizability (GCPM) with ab initio Car-Parrinello molecular dynamics (CPMD) simulations. We compare the total dipole moment, the total dipole moment distribution, and degree of hydrogen bonding at ambient to supercritical conditions. We also compared the total dipole moment calculated from both the electron density (partitioning the electron density among molecules based on a zero electron flux condition), and from the center of localized Wannier function centers (WFCs). Compared to CPMD, we found that GCPM overpredicts the dipole moment derived by partitioning the electron density and underpredicts that obtained from the WFCs, but exhibits similar trends and distribution of values. We also found that GCPM predicted similar degrees of hydrogen bonding compared to CPMD and has a similar structure.

  12. A Coarse-Grained Molecular Dynamics Simulation Using NAMD Package to Reveal Aggregation Profile of Phospholipids Self-Assembly in Water

    Directory of Open Access Journals (Sweden)

    Dwi Hudiyanti

    2014-01-01

    Full Text Available The energy profile of self-assembly process of DLPE, DLPS, DOPE, DOPS, DLiPE, and DLiPS in water was investigated by a coarse-grained molecular dynamics simulation using NAMD package. The self-assembly process was initiated from random configurations. The simulation was carried out for 160 ns. This study presented proof that there were three major self-assembled arrangements which became visible for a certain duration when the simulation took place, that is, liposome, deformed liposome, and planar bilayer. The energy profile that shows plateau at the time of these structures emerge confirmed their stability therein. Our findings have highlighted the idea that liposomes and deformed liposomes are metastable phases which eventually will turn into planar bilayer, the stable one.

  13. Molecular dynamics simulation of the cooperative adsorption of barley lipid transfer protein and cis-isocohumulone at the vacuum-water interface.

    Science.gov (United States)

    Euston, S R; Hughes, P; Naser, Md A; Westacott, R E

    2008-11-01

    Molecular dynamic simulations have been carried out on systems containing a mixture of barley lipid transfer protein (LTP) and cis-isocohumulone (a hop derived iso-alpha-acid) in one of its enol forms, in bulk water and at the vacuum-water interface. In solution, the cis-isocohumulone molecules bind to the surface of the LTP molecule. The mechanism of binding appears to be purely hydrophobic in nature via desolvation of the protein surface. Binding of hop acids to the LTP leads to a small change in the 3-D conformation of the protein, but no change in the proportion of secondary structure present in helices, even though there is a significant degree of hop acid binding to the helical regions. At the vacuum-water interface, cis-isocohumulone shows a high surface activity and adsorbs rapidly at the interface. LTP then shows a preference to bind to the preadsorbed hop acid layer at the interface rather than to the bare water-vacuum interface. The free energy of adsorption of LTP at the hop-vacuum-water interface is more favorable than for adsorption at the vacuum-water interface. Our results support the view that hop iso-alpha-acids promote beer foam stability by forming bridges between separate adsorbed protein molecules, thus strengthening the adsorbed protein layer and reducing foam breakdown by lamellar phase drainage. The results also suggest a second mechanism may also occur, whereby the concentration of protein at the interface is increased via enhanced protein adsorption to adsorbed hop acid layers. This too would increase foam stability through its effect on the stabilizing protein layer around the foam bubbles.

  14. A coarse-grain molecular dynamics study of oil-water interfaces in the presence of silica nanoparticles and nonionic surfactants

    Science.gov (United States)

    Katiyar, Parul; Singh, Jayant K.

    2017-05-01

    In this work, we have studied the effect of hydrophilic silica nanoparticles (NPs), in the presence of nonionic surfactants (Triethylene glycol monododecyl ether and Tween 20), on the oil-water (n-octane-water, n-dodecane-water and n-hexadecane-water) interfacial tensions (IFTs) at 300 K, using coarse-grained molecular dynamics simulations based on the MARTINI force field. Simulation results indicate that silica NPs solely do not affect the IFT. However, the silica NPs may or may not increase the IFT of oil-water containing nonionic surfactant, depending on the tendency of the surfactant to adsorb on the surface of NPs. The adsorption occurs due to the formation of hydrogen bonds, and adsorption increases with a decrease in pH, as seen in experimental studies. In this work, we found that the oil-water IFT increases with an increasing amount of adsorption of the surfactant on NPs. At a fixed amount of adsorption of the surfactant on NPs, the IFT behavior is indifferent to the change in concentration of NPs. However, the IFT decreases with an increase in surfactant concentration. We present a detailed analysis of the density profile and intrinsic width of the interface. The IFT behavior is found to correlate extremely well with the intrinsic width of the interface. The current study provides an explanation for the increase in IFT observed in a recent experiment [N. R. Biswal et al., J. Phys. Chem. B 120, 7265-7274 (2016)] for various types of NPs and nonionic surfactant systems.

  15. Molecular Biodynamers : Dynamic Covalent Analogues of Biopolymers

    NARCIS (Netherlands)

    Liu, Yun; Lehn, Jean-Marie; Hirsch, Anna K H

    2017-01-01

    Constitutional dynamic chemistry (CDC) features the use of reversible linkages at both molecular and supramolecular levels, including reversible covalent bonds (dynamic covalent chemistry, DCC) and noncovalent interactions (dynamic noncovalent chemistry, DNCC). Due to its inherent reversibility and

  16. Molecular Biodynamers : Dynamic Covalent Analogues of Biopolymers

    NARCIS (Netherlands)

    Liu, Yun; Lehn, Jean-Marie; Hirsch, Anna K H

    2017-01-01

    Constitutional dynamic chemistry (CDC) features the use of reversible linkages at both molecular and supramolecular levels, including reversible covalent bonds (dynamic covalent chemistry, DCC) and noncovalent interactions (dynamic noncovalent chemistry, DNCC). Due to its inherent reversibility and

  17. Development of a molecular-dynamics-based cluster-heat-capacity model for study of homogeneous condensation in supersonic water-vapor expansions.

    Science.gov (United States)

    Borner, Arnaud; Li, Zheng; Levin, Deborah A

    2013-02-14

    Supersonic expansions to vacuum produce clusters of sufficiently small size that properties such as heat capacities and latent heat of evaporation cannot be described by bulk vapor thermodynamic values. In this work the Monte-Carlo Canonical-Ensemble (MCCE) method was used to provide potential energies and constant-volume heat capacities for small water clusters. The cluster structures obtained using the well-known simple point charge model were found to agree well with earlier simulations using more rigorous potentials. The MCCE results were used as the starting point for molecular dynamics simulations of the evaporation rate as a function of cluster temperature and size which were found to agree with unimolecular dissociation theory and classical nucleation theory. The heat capacities and latent heat obtained from the MCCE simulations were used in direct-simulation Monte-Carlo of two experiments that measured Rayleigh scattering and terminal dimer mole fraction of supersonic water-jet expansions. Water-cluster temperature and size were found to be influenced by the use of kinetic rather than thermodynamic heat-capacity and latent-heat values as well as the nucleation model.

  18. Molecular dynamics insights into the structural and diffusive properties of ZIF-8/PDMS mixed matrix membranes in the n-butanol/water pervaporation process

    Science.gov (United States)

    Sun, Tao; Fang, Manquan; Wu, Zhen; Yu, Lixin; Li, Jiding

    2017-04-01

    Molecular dynamics (MD) simulation was used to study the structural and diffusive properties of zeolitic imidazolate framework-8 (ZIF-8)/polydimethylsiloxane (PDMS), a novel alcohol-permselective mixed matrix membrane (MMM). Simulation models of one pure PDMS membrane and three ZIF-8/PDMS MMMs with increasing loadings were successfully constructed. Non-bond energy turned out to be a strong attractive interaction between the PDMS matrix and ZIF-8 cells. The morphology and mobility of PDMS chains were characterized by mean square displacement (MSD). The fraction of free volume (FFV) of the pure membrane and MMMs was calculated and showed declining trends with increasing ZIF-8 loadings. The diffusion coefficients of n-butanol and water molecules were calculated by the Einstein relation. {D}n-\\text{butanol} first increased then decreased, while {D}{{water}} decreased with the increasing loadings. The mechanism of selective diffusion behaviour was investigated and it was found that the inner channels of ZIF-8 provided selective pathways for n-butanol. Diffusion coefficients were correlated with FFV and the results showed that the logarithm of {D}{{water}} demonstrated a good linear relation with the inverse FFV and was in agreement with the free volume theory, while {D}n-\\text{butanol} showed a significant deviation in the case of MMM-1 due to the selective diffusion channels provided by ZIF-8.

  19. Path integral molecular dynamic study of nuclear quantum effect on small chloride water clusters of Cl-(H2O)1-4

    Science.gov (United States)

    Wang, Qi; Suzuki, Kimichi; Nagashima, Umpei; Tachikawa, Masanori; Yan, Shiwei

    2013-06-01

    The nuclear quantum effect, which plays important roles on ionic hydrogen bonded structures of Cl-(H2O)n (n = 1-4) clusters, was explored by carrying out path integral molecular dynamic simulations. An outer shell coordinate rl(Cl⋯O) is selected to display the rearrangement of single and multi hydration shell cluster structures. By incorporating the nuclear quantum effect, it is shown that the probability for single shell structures is decreased while the probability for multi shell structures is increased. On the other hand, the correlations between changing of bonded H∗ atom to Cl- (defined as δ) and other cluster vibration coordinates are studied. We have found that δ strongly correlates with proton transfer motion while it has little correlation with ion-water stretching motion. Contrary to θ(H-O-H∗) coordinate, the correlations between δ and other coordinates are decreased by inclusion of nuclear quantum effect. The results indicate that the water-water hydrogen bond interactions are encouraged by quantum simulations.

  20. Molecular Dynamics Simulation for Surface and Transport Properties of Fluorinated Silica Nanoparticles in Water or Decane: Application to Gas Recovery Enhancement

    Directory of Open Access Journals (Sweden)

    Sepehrinia Kazem

    2017-05-01

    Full Text Available Determination of surface and transport properties of nanoparticles (NPs is essential for a variety of applications in enhanced oil and gas recoveries. In this paper, the impact of the surface chemistry of silica NPs on their hydro- and oleo-phobic properties as well as their transport properties are investigated in water or decane using molecular dynamics simulation. Trifluoromethyl or pentafluoroethyl groups as water and oil repellents are placed on the NPs. It is found that the density and residence time of liquid molecules around the NPs are modulated considerably with the existence of the functional groups on the NPs’ surfaces. Also, much larger density fluctuations for liquids close to the surface of the NPs are observed when the number of the groups on the NPs increases, indicating increased hydrophobicity. In addition, the diffusion coefficient of the NPs in either water or decane increases with increasing the number or length of the fluorocarbon chains, demonstrating non-Brownian behavior for the NPs. The surface chemistry imparts a considerable contribution on the diffusion coefficient of the NPs. Finally, potential of mean force calculations are undertaken. It is observed that the free energy of adsorption of the NPs on a mineral surface is more favorable than that of the aggregation of the NPs, which suggests the NPs adsorb preferably on the mineral surface.

  1. Determination of the effects of water adsorption on the sensitivity and detonation performance of the explosive JOB-9003 by molecular dynamics simulation.

    Science.gov (United States)

    Hang, GuiYun; Yu, WenLi; Wang, Tao; Li, Zhen

    2016-11-01

    In order to determine the adsorption mechanism of water on the crystal surfaces of the explosive JOB-9003 and the effect of this adsorption on the sensitivity and detonation performance of this explosive, a model of the crystal of JOB-9003 was created in the software package Materials Studio (MS). The adsorption process was simulated, and molecular dynamics simulation was performed with the COMPASS force field in the NPT ensemble to calculate the sensitivity and detonation performance of the explosive. The results show that the maximum trigger bond length decreases whereas the interaction energy of the trigger bond and the cohesive energy density increase after adsorption, indicating that the sensitivity of JOB-9003 decreases. The results for the detonation performance show that the detonation pressure, detonation velocity, and detonation heat decrease upon the adsorption of water, thus illustrating that the detonation performance of JOB-9003 is degraded. In summary, the adsorption of water has a positive effect on the sensitivity and safety of the explosive JOB-9003 but a negative effect on its detonation performance.

  2. Scalable molecular dynamics with NAMD.

    Science.gov (United States)

    Phillips, James C; Braun, Rosemary; Wang, Wei; Gumbart, James; Tajkhorshid, Emad; Villa, Elizabeth; Chipot, Christophe; Skeel, Robert D; Kalé, Laxmikant; Schulten, Klaus

    2005-12-01

    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 article, 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. Finally, typical NAMD use is illustrated with representative applications to a small, a medium, and a large biomolecular system, highlighting particular features of NAMD, for example, the Tcl scripting language. The article also 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. (c) 2005 Wiley Periodicals, Inc.

  3. Rheology via nonequilibrium molecular dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Hoover, W.G.

    1982-10-01

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

  4. Better, Cheaper, Faster Molecular Dynamics

    Science.gov (United States)

    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.

  5. Molecular dynamics of interface rupture

    Science.gov (United States)

    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.

  6. Molecular dynamics of interface rupture

    Science.gov (United States)

    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.

  7. Direct phase coexistence molecular dynamics study of the phase equilibria of the ternary methane-carbon dioxide-water hydrate system.

    Science.gov (United States)

    Michalis, Vasileios K; Tsimpanogiannis, Ioannis N; Stubos, Athanassios K; Economou, Ioannis G

    2016-09-14

    Molecular dynamics simulation is used to predict the phase equilibrium conditions of a ternary hydrate system. In particular, the direct phase coexistence methodology is implemented for the determination of the three-phase coexistence temperature of the methane-carbon dioxide-water hydrate system at elevated pressures. The TIP4P/ice, TraPPE-UA and OPLS-UA forcefields for water, carbon dioxide and methane respectively are used, in line with our previous studies of the phase equilibria of the corresponding binary hydrate systems. The solubility in the aqueous phase of the guest molecules of the respective binary and ternary systems is examined under hydrate-forming conditions, providing insight into the predictive capability of the methodology as well as the combination of these forcefields to accurately describe the phase behavior of the ternary system. The three-phase coexistence temperature is calculated at 400, 1000 and 2000 bar for two compositions of the methane-carbon dioxide mixture. The predicted values are compared with available calculations with satisfactory agreement. An estimation is also provided for the fraction of the guest molecules in the mixed hydrate phase under the conditions examined.

  8. Binding structure and kinetics of surfactin monolayer formed at the air/water interface to counterions: A molecular dynamics simulation study.

    Science.gov (United States)

    Gang, Hongze; Liu, Jinfeng; Mu, Bozhong

    2015-10-01

    The binding structure and kinetics of ionized surfactin monolayer formed at the air/water interface to five counterions, Li+, Na+, K+, Ca2+, and Ba2+ (molar ratios of surfactin to monovalent and divalent counterions are 1:2 and 1:1 respectively), have been studied using molecular dynamics simulation. The results show that surfactin exhibits higher binding affinity to divalent counterions, Ca2+, and Ba2+, and smaller monovalent counterion, Li+, than Na+ and K+. Both carboxyl groups in surfactin are accessible for counterions, but the carboxyl group in Glu1 is easier to access by counterions than Asp5. Salt bridges are widely built between carboxyl groups by counterions, and the probability of the formation of intermolecular salt bridge is markedly larger than that of intramolecular salt bridge. Divalent counterions perform well in forming salt bridges between carboxyl groups. The salt bridges mediated by Ca2+ are so rigid that the lifetimes are about 0.13 ns, and the break rates of these salt bridges are 1-2 orders of magnitude smaller than those mediated by K+ which is about 5 ps in duration. The positions of the hydration layer of carboxyl groups are independent of counterions, but the bound counterions induce the dehydration of carboxyl groups and disturb the hydrogen bonds built between carboxyl group and hydration water.

  9. Prediction of cyclohexane-water distribution coefficients for the SAMPL5 data set using molecular dynamics simulations with the OPLS-AA force field

    Science.gov (United States)

    Kenney, Ian M.; Beckstein, Oliver; Iorga, Bogdan I.

    2016-11-01

    All-atom molecular dynamics simulations were used to predict water-cyclohexane distribution coefficients D_{cw} of a range of small molecules as part of the SAMPL5 blind prediction challenge. Molecules were parameterized with the transferable all-atom OPLS-AA force field, which required the derivation of new parameters for sulfamides and heterocycles and validation of cyclohexane parameters as a solvent. The distribution coefficient was calculated from the solvation free energies of the compound in water and cyclohexane. Absolute solvation free energies were computed by an established protocol using windowed alchemical free energy perturbation with thermodynamic integration. This protocol resulted in an overall root mean square error in log D_{cw} of almost 4 log units and an overall signed error of -3 compared to experimental data. There was no substantial overall difference in accuracy between simulating in NVT and NPT ensembles. The signed error suggests a systematic error but the experimental D_{cw} data on their own are insufficient to uncover the source of this error. Preliminary work suggests that the major source of error lies in the hydration free energy calculations.

  10. Temperature-dependent phase transition and desorption free energy of sodium dodecyl sulfate at the water/vapor interface: approaches from molecular dynamics simulations.

    Science.gov (United States)

    Chen, Meng; Lu, Xiancai; Liu, Xiandong; Hou, Qingfeng; Zhu, Youyi; Zhou, Huiqun

    2014-09-09

    Adsorption of surfactants at the water/vapor interface depends upon their chemical potential at the interface, which is generally temperature-dependent. Molecular dynamics simulations have been performed to reveal temperature influences on the microstructure of sodium dodecyl sulfate (SDS) molecule adsorption layer. At room temperature, SDS molecules aggregate at the interface, being in a liquid-expanded phase, whereas they tend to spread out and probably transit to a gaseous phase as the temperature increases to above 318 K. This phase transition has been confirmed by the temperature-dependent changes in two-dimensional array, tilt angles, and immersion depths to the aqueous phase of SDS molecules. The aggregation of SDS molecules accompanies with larger immersion depths, more coordination of Na(+) ions, and less coordination of water. Desorption free energy profiles show that higher desorption free energy appears for SDS molecules at the aggregate state at low temperatures, but no energy barrier is observed. The shapes of desorption free energy profiles depend upon the distribution of SDS at the interface, which, in turn, is related to the phase state of SDS. Our study sheds light on the development of adsorption thermodynamics and kinetics theories.

  11. All-atom Molecular Dynamic Simulations Combined with the Chemical Shifts Study on the Weak Interactions of Ethanol-water System

    Institute of Scientific and Technical Information of China (English)

    ZHANG Rong; LUO San-Lai; WU Wen-Juan

    2008-01-01

    All-atom molecular dynamics(MD)simulation combined with chemical shifts was performed to investigate the interactions over the entire concentration range of the ethanol(EtOH)-water system.The results of the simulation were adopted to explain the NMR experiments by hydrogen bonding analysis.The strong hydrogen bonds and weak C-H…O contacts coexist in the mixtures through the analysis of the radial distribution functions.And the liquid structures in the whole concentration of EtOH-water mixtures can be classified into three regions by the statistic analysis of the hydrogen-bonding network in the MD simulations.Moreover,the chemical shifts of the hydrogen atom are in agreement witb the statistical results of the average number hydrogen bonds in the MD simulations.Interestingly,the excess relative extent Eηrel calculated by the MD simulations and chemical shifts in the EtOH aqueous solutions shows the largest deviation at XEtOH≈0.18.The excess properties present good agreement with the excess enthalpy in the concentration dependence.

  12. A Study of the Solvation Structure of L-Leucine in Alcohol-Water Binary Solvents through Molecular Dynamics Simulations and FTIR and NMR Spectroscopy.

    Science.gov (United States)

    Takamuku, Toshiyuki; Hatomoto, Yohei; Tonegawa, Junko; Tsutsumi, Youichi; Umecky, Tatsuya

    2015-10-26

    The solvation structures of l-leucine (Leu) in aliphatic-alcohol-water and fluorinated-alcohol-water solvents are elucidated for various alcohol contents by using molecular dynamics (MD) simulations and IR, and (1) H and (13) C NMR spectroscopy. The aliphatic alcohols included methanol, ethanol, and 2-propanol, whereas the fluorinated alcohols were 2,2,2-trifluoroethanol and 1,1,1,3,3,3-hexafluoro-2-propanol. The MD results show that the hydrophobic alkyl moiety of Leu is surrounded by the alkyl or fluoroalkyl groups of the alcohol molecules. In particular, TFE and HFIP significantly solvate the alkyl group of Leu. IR spectra reveal that the Leu C-H stretching vibration blueshifts in fluorinated alcohol solutions with increasing alcohol content, whereas the vibration redshifts in aliphatic alcohol solutions. When the C-H stretching vibration blueshifts in the fluorinated alcohol solutions, the hydrogen and carbon atoms of the Leu alkyl group are magnetically shielded. Consequently, TFE and HFIP molecules may solvate the Leu alkyl group through the blue-shifting hydrogen bonds.

  13. Dynamics of Water Entry

    CERN Document Server

    Truscott, Tadd T; Techet, Alexandra H

    2008-01-01

    The hydrodynamics associated with water-entry of spheres can be highly variable with respect to the material and kinematic properties of the sphere. This series of five fluid dynamics videos illustrates several subtle but interesting variations that can be seen. The first series of videos contrasts the nature of impact ($Fr = U_o/\\sqrt{gd} = 5.15$) between a hydrophilic (wetting angle of $\\alpha$ = 60$^\\circ$) and hydrophobic sphere ($\\alpha$ = 120$^\\circ$), and illustrates how surface coating can affect whether or not an air cavity is formed; the views from the side and from above are synchronized in time. The second video series illustrates how spin and surface treatments can alter the splash and cavity formation following water entry. The spinning sphere ($S = \\omega r / U_o = 1.7$; $Fr = 5.15$) causes a wedge of fluid to be drawn into the cavity due to the no-slip condition and follows a curved trajectory. The non-spinning sphere ($Fr = 5.15$) has two distinct surface treatments on the left and right hemi...

  14. All-atom Molecular Dynamic Simulations and NMR Spectra Study on Intermolecular Interactions of N,N-dimethylacetamide-Water System

    Institute of Scientific and Technical Information of China (English)

    Rong Zhang; Zai-you Tan; San-lai Luo

    2008-01-01

    N,N-dimethylacetamide (DMA) has been investigated extensively in studying models of peptide bonds. An all-atom MD simulation and the NMR spectra were performed to investigate the interactions in the DMA- water system. The radial distribution functions (RDFs) and the hydrogen-bonding network were used in MD simulations. There are strong hydrogen bonds and weak C-H…O contacts in the mixtures, as shown by the analysis of the RDFs. The insight structures in the DMA-water mixtures can be classified into different regions by the analysis of the hydrogen-bonding network. Chemical shifts of the hydrogen atom of water molecule with concentration and temperatures are adopted to study the interactions in the mixtures. The results of NMR spectra show good agreement with the statistical results of hydrogen bonds in MD simulations.

  15. Calcite surface structure and reactivity: molecular dynamics simulations and macroscopic surface modelling of the calcite-water interface

    NARCIS (Netherlands)

    Wolthers, M.; Di Tommaso, D.; Du, Z.; de Leeuw, N.H.

    2012-01-01

    Calcite–water interactions are important not only in carbon sequestration and the global carbon cycle, but also in contaminant behaviour in calcite-bearing host rock and in many industrial applications. Here we quantify the effect of variations in surface structure on calcite surface reactivity. Fir

  16. A molecular dynamics study of nanoconfined water flow driven by rotating electric fields under realistic experimental conditions

    DEFF Research Database (Denmark)

    De Luca, Sergio; Todd, Billy; Hansen, Jesper Schmidt;

    2014-01-01

    by an external spatially uniform rotating electric field and confined between two planar surfaces exposing different degrees of hydrophobicity. The permanent dipole moment of water follows the rotating field, thus inducing the molecules to spin, and the torque exerted by the field is continuously injected...... into the fluid, enabling a steady conversion of spin angular momentum into linear momentum. The translational–rotational coupling is a sensitive function of the rotating electric field parameters. In this work, we have found that there exists a small energy dissipation region attainable when the frequency...... of the rotating electric field matches the inverse of the dielectric relaxation time of water and when its amplitude lies in a range just before dielectric saturation effects take place. In this region, that is, when the frequency lies in a small window of the microwave region around ∼20 GHz and amplitude ∼0.03 V...

  17. Water structure as a function of temperature from X-ray scatteringexperiments and ab initio molecular dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Hura, Greg; Russo, Daniela; Glaeser, Robert M.; Head-Gordon,Teresa; Krack, Matthias; Parrinello, Michele

    2003-03-01

    We present high-quality X-ray scattering experiments on pure water taken over a temperature range of 2 to 77 C using a synchrotron beam line at the advanced light source (ALS) at Lawrence Berkeley National Laboratory. The ALS X-ray scattering intensities are qualitatively different in trend of maximum intensity over this temperature range compared to older X-ray experiments. While the common procedure is to report both the intensity curve and radial distribution function(s), the proper extraction of the real-space pair correlation functions from the experimental scattering is very difficult due to uncertainty introduced in the experimental corrections, the proper weighting of OO, OH, and HH contributions, and numerical problems of Fourier transforming truncated data in Q-space. Instead, we consider the direct calculation of X-ray scattering spectra using electron densities derived from density functional theory based on real-space configurations generated with classical water models. The simulation of the experimental intensity is therefore definitive for determining radial distribution functions over a smaller Q-range. We find that the TIP4P, TIP5P and polarizable TIP4P-Pol2 water models, with DFT-LDA densities, show very good agreement with the experimental intensities, and TIP4P-Pol2 in particular shows quantitative agreement over the full temperature range. The resulting radial distribution functions from TIP4P-Pol2 provide the current best benchmarks for real-space water structure over the biologically relevant temperature range studied here.

  18. Molecular dynamics simulations of structure-property relationships of Tween 80 surfactants in water and at interfaces.

    Science.gov (United States)

    Tang, Xueming; Huston, Kyle J; Larson, Ronald G

    2014-11-13

    We build a united atom model for Tween 80 (polyoxyethylene sorbitan oleates), based on the GROMOS53A6(OXY+D) force field, and apply it to two stereoisomers, three constitutional isomers, and three structures with one, two, and three tails, to represent components in the Tween 80 commercial mixture. In a preassembled micelle containing 60 molecules, the distribution of Tween tail and ethylene oxide head groups is found to be insensitive to stereoisomerization but sensitive to changes in relative lengths of the four polyoxyethylene head groups. At the air-water and oil-water interfaces, the interfacial tension is significantly lower for the constitutional isomer with a shorter W headgroup, which attaches the tail to the sorbitan ring, and for Tween 80 isomers with more than one tail group. The results indicate the possible scope for improvement in the design of polyoxyethylene sorbitan oleates with improved surface tension reduction or better spreading at the oil-water interface. We also report surfactant component distribution profiles within preassembled micelles and at interfaces that can be used for validating coarse-grained surfactant models needed for simulation of self-assembly of Tween 80 surfactant mixtures.

  19. Molecular Dynamics and Picosecond Vibrational Spectra.

    Science.gov (United States)

    1980-07-01

    and Identify by block number) molecular dynamics picosecond infra-red spectra crmputer simulation vibrational spectra array processor linear rcsponse...that for molecular dynamics theoretical computation is now long enough, to significantly overlap. This overlap of theory and experiment can, at least...to discover these microscopic atomic trajectories, i.e. the molecular dynamics of solution processes, we must be able to both theoretically compute

  20. Molecular Dynamics in the Vacuum Ultraviolet

    Science.gov (United States)

    1989-01-30

    CLASSIFICATION OF THIS PAGE COMPLETED PROJECT SUMMARY TITLE: Molecular dynamics in the Vacuum Ultraviolet PRINCIPAL INVESTIGATOR: Paul L. Houston...DTIC TAB 0 Unannounced 0 By Distr ibution I Availability Codes Avail and I or Dist Special I Molecular Dynamics In the Vacuum Ultraviolet Final Technical...Further development of tunable vacuum ultraviolet sources has opened wide areas of molecular dynamics for study. Completed Research Photodissociation of

  1. Full molecular dynamics simulations of liquid water and carbon tetrachloride for two-dimensional Raman spectroscopy in the frequency domain

    CERN Document Server

    Jo, Ju-Yeon; Tanimura, Yoshitaka

    2016-01-01

    Frequency-domain two-dimensional Raman signals, which are equivalent to coherent two-dimensional Raman scattering (COTRAS) signals, for liquid water and carbon tetrachloride were calculated using an equilibrium-nonequilibrium hybrid MD simulation algorithm. We elucidate mechanisms governing the 2D signal pro?les involving anharmonic mode-mode coupling and the nonlinearities of the polarizability for the intermolecular and intramolecular vibrational modes. The predicted signal pro?les and intensities can be utilized to analyze recently developed single-beam 2D spectra, whose signals are generated from a coherently controlled pulse, allowing the single-beam measurement to be carried out more efficiently.

  2. Molecular dynamics simulation of benzene

    Science.gov (United States)

    Trumpakaj, Zygmunt; Linde, Bogumił B. J.

    2016-03-01

    Intermolecular potentials and a few models of intermolecular interaction in liquid benzene are tested by Molecular Dynamics (MD) simulations. The repulsive part of the Lennard-Jones 12-6 (LJ 12-6) potential is too hard, which yields incorrect results. The exp-6 potential with a too hard repulsive term is also often used. Therefore, we took an expa-6 potential with a small Gaussian correction plus electrostatic interactions. This allows to modify the curvature of the potential. The MD simulations are carried out in the temperature range 280-352 K under normal pressure and at experimental density. The Rayleigh scattering of depolarized light is used for comparison. The results of MD simulations are comparable with the experimental values.

  3. Brownian motion from molecular dynamics

    CERN Document Server

    Shin, Hyun Kyung; Talkner, Peter; Lee, Eok Kyun

    2010-01-01

    Brownian motion of single particles with various masses M and diameters D is studied by molecular dynamics simulations. Besides the momentum auto-correlation function of the Brownian particle the memory function and the fluctuating force which enter the generalized Langevin equation of the Brownian particle are determined and their dependence on mass and diameter are investigated for two different fluid densities. Deviations of the fluctuating force distribution from a Gaussian form are observed for small particle diameters. For heavy particles the deviations of the fluctuating force from the total force acting on the Brownian particle decrease linearly with the mass ratio m/M where m denotes the mass of a fluid particle.

  4. 外电场作用下柔性模型水的分子动力学模拟%Effect of an external electric field on liquid water using molecular dynamics simulation with a flexible potential

    Institute of Scientific and Technical Information of China (English)

    孙炜; 陈中; 黄素逸

    2006-01-01

    Molecular dynamics simulations of liquid water were performed at 258 K and density of 1.0 g/cm3 under different strengths of an external electric field, ranging from 0 to 8.0 × 109 V/m, to investigate the influence of an external field on structural and dynamic properties of water.The flexible simple point charge model is used for water molecules.An enhancement of the water hydrogen bond structure with increasing strength of the electric field has been deduced from the radial distribution functions and the analysis of hydrogen bond structure.With increasing field strength, water system has a more perfect structure, which is similar to ice structure.However, the electrofreezing phenomenon of liquid water has not been detected because of a too large self-diffusion coefficient.The self-diffusion coefficient decreases remarkably with increasing strength of electric field, and the self-diffusion coefficient is anisotropic.

  5. Theoretical Concepts in Molecular Photodissociation Dynamics

    DEFF Research Database (Denmark)

    Henriksen, Niels Engholm

    1995-01-01

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

  6. Molecular dynamics of membrane proteins.

    Energy Technology Data Exchange (ETDEWEB)

    Woolf, Thomas B. (Johns Hopkins University School of Medicine, Baltimore, MD); 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.

  7. Programming an Interpreter Using Molecular Dynamics

    Directory of Open Access Journals (Sweden)

    C.A. Middelburg

    2007-01-01

    Full Text Available PGA (ProGram Algebra is an algebra of programs which concerns programs in their simplest form: sequences of instructions. Molecular dynamics is a simple model of computation developed in the setting of PGA, which bears on the use of dynamic data structures in programming.We consider the programming of an interpreter for a program notation that is close to existing assembly languages using PGA with the primitives of molecular dynamics as basic instructions. It happens that, although primarily meant for explaining programming language features relating to the use of dynamic data structures, the collection of primitives of molecular dynamics in itself is suited to our programming wants.

  8. A MOLECULAR-DYNAMICS STUDY OF LECITHIN MONOLAYERS

    NARCIS (Netherlands)

    AHLSTROM, P; BERENDSEN, HJC

    1993-01-01

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

  9. A study on the structural features of SELK, an over-expressed protein in hepatocellular carcinoma, by molecular dynamics simulations in a lipid-water system.

    Science.gov (United States)

    Polo, Andrea; Guariniello, Stefano; Colonna, Giovanni; Ciliberto, Gennaro; Costantini, Susan

    2016-10-20

    Human SELK is a small trans-membrane selenoprotein characterized by a single trans-membrane helix, while the N-terminal region protrudes into the lumen and the long C-terminal domain into the cytoplasm. SELK is over-expressed in some cancers, like hepatocellular carcinoma; however its precise role in cancer development is presently unknown. SELK is involved in promoting the calcium flux, catalyzing palmitoylation reactions and protein degradation in the endoplasmic reticulum (ER). Therefore, this protein should bind many different proteins like p97/VCP in the supramolecular complex involved in the ER degradation pathway. To study the structural features of SELK in the membrane, we have modeled the protein and then subjected it to molecular dynamics simulations in a lipid-water system. The model shows a N-terminal domain with three β-strands and a short helix, a well-defined trans-membrane helix and a C-terminal domain that lacks a persistent secondary structure and contains long disordered regions. The trajectory analysis during the simulation evidences that: (i) the N-terminal region explores a limited conformational space and is stabilized by intra-peptide H-bonds as well with membrane lipids and water, (ii) the trans-membrane helix was found to be quite stable and (iii) the disordered C-terminal region is stabilized by H-bonds with clustered water molecules as well as by rapidly interchanging intra-peptidic H-bonds, with a structural tendency to compact around the four HUB residues found for this domain. Moreover, N-terminal and C-terminal clusters are distributed differently in the conformational space suggesting that their dynamics are coupled complicatedly through the membrane. Further analyses have shown that the N-terminal has a tendency to pivot around the insertion with the TM-helix through the fluctuations of the three β-strands, which, in turn, show features similar to WW-domains. These results will be useful to study the SELK, SELS and VCP complex

  10. The electric double layer at a rutile TiO₂ water interface modelled using density functional theory based molecular dynamics simulation.

    Science.gov (United States)

    Cheng, J; Sprik, M

    2014-06-18

    A fully atomistic model of a compact electric double layer at the rutile TiO2(1 1 0)-water interface is constructed by adding protons to bridging oxygens or removing them from H2O molecules adsorbed on terminal metal cation sites. The surface charge is compensated by F(-) or Na(+) counter ions in outer as well as inner sphere coordination. For each of the protonation states the energy of the TiO2 conduction band minimum is determined relative to the standard hydrogen electrode by computing the free energy for the combined insertion of an electron in the solid and a proton in solution away from the double layer using density functional theory based molecular dynamics methods. Interpreted as electrode potentials, this gives an estimate of the capacitance which is compared to the capacitance obtained from the difference in the average electrostatic potentials in the solid and aqueous phase. When aligned at the point of zero charge these two methods lead to almost identical potential-charge profiles. We find that inner sphere complexes have a slightly larger capacitance (0.4 F m(-2)) compared to outer sphere complexes (0.3 F m(-2)).

  11. Folding and translocation of the undecamer of poly-L-leucine across the water-hexane interface. A molecular dynamics study

    Science.gov (United States)

    Chipot, C.; Pohorille, A.

    1998-01-01

    The undecamer of poly-L-leucine at the water-hexane interface is studied by molecular dynamics simulations. This represents a simple model relevant to folding and insertion of hydrophobic peptides into membranes. The peptide, initially placed in a random coil conformation on the aqueous side of the system, rapidly translocates toward the hexane phase and undergoes interfacial folding into an alpha-helix in the subsequent 36 ns. Folding is nonsequential and highly dynamic. The initially formed helical segment at the N-terminus of the undecamer becomes transiently broken and, subsequently, reforms before the remainder of the peptide folds from the C-terminus. The formation of intramolecular hydrogen bonds during the folding of the peptide is preceded by a dehydration of the participating polar groups, as they become immersed in hexane. Folding proceeds through a short-lived intermediate, a 3(10)-helix, which rapidly interconverts to an alpha-helix. Both helices contribute to the equilibrium ensemble of folded structures. The helical peptide is largely buried in hexane, yet remains adsorbed at the interface. Its preferred orientation is parallel to the interface, although the perpendicular arrangement with the N-terminus immersed in hexane is only slightly less favorable. In contrast, the reversed orientation is highly unfavorable, because it would require dehydration of C-terminus carbonyl groups that do not participate in intramolecular hydrogen bonding. For the same reason, the transfer of the undecamer from the interface to the bulk hexane is also unfavorable. The results suggest that hydrophobic peptides fold in the interfacial region and, simultaneously, translocate into the nonpolar side of the interface. It is further implied that peptide insertion into the membrane is accomplished by rotating from the parallel to the perpendicular orientation, most likely in such a way that the N-terminus penetrates the bilayer.

  12. The Role of Water in Activation Mechanism of Human N-Formyl Peptide Receptor 1 (FPR1) Based on Molecular Dynamics Simulations

    Science.gov (United States)

    Yuan, Shuguang; Ghoshdastider, Umesh; Trzaskowski, Bartosz; Latek, Dorota; Debinski, Aleksander; Pulawski, Wojciech; Wu, Rongliang; Gerke, Volker; Filipek, Slawomir

    2012-01-01

    The Formyl Peptide Receptor 1 (FPR1) is an important chemotaxis receptor involved in various aspects of host defense and inflammatory processes. We constructed a model of FPR1 using as a novel template the chemokine receptor CXCR4 from the same branch of the phylogenetic tree of G-protein-coupled receptors. The previously employed template of rhodopsin contained a bulge at the extracellular part of TM2 which directly influenced binding of ligands. We also conducted molecular dynamics (MD) simulations of FPR1 in the apo form as well as in a form complexed with the agonist fMLF and the antagonist tBocMLF in the model membrane. During all MD simulation of the fMLF-FPR1 complex a water molecule transiently bridged the hydrogen bond between W2546.48 and N1083.35 in the middle of the receptor. We also observed a change in the cytoplasmic part of FPR1 of a rotamer of the Y3017.53 residue (tyrosine rotamer switch). This effect facilitated movement of more water molecules toward the receptor center. Such rotamer of Y3017.53 was not observed in any crystal structures of GPCRs which can suggest that this state is temporarily formed to pass the water molecules during the activation process. The presence of a distance between agonist and residues R2015.38 and R2055.42 on helix TM5 may suggest that the activation of FPR1 is similar to the activation of β-adrenergic receptors since their agonists are separated from serine residues on helix TM5. The removal of water molecules bridging these interactions in FPR1 can result in shrinking of the binding site during activation similarly to the shrinking observed in β-ARs. The number of GPCR crystal structures with agonists is still scarce so the designing of new ligands with agonistic properties is hampered, therefore homology modeling and docking can provide suitable models. Additionally, the MD simulations can be beneficial to outline the mechanisms of receptor activation and the agonist/antagonist sensing. PMID:23189124

  13. What determines water-bridge lifetimes at the surface of DNA? Insight from systematic molecular dynamics analysis of water kinetics for various DNA sequences.

    Science.gov (United States)

    Yonetani, Yoshiteru; Kono, Hidetoshi

    2012-01-01

    The lifetime during which a water molecule resides at the surface of a biomolecule varies according to the hydration site. What determines this variety of lifetimes? Despite many previous studies, there is still no uniform picture quantitatively explaining this phenomenon. Here we calculate the lifetime for a particular hydration pattern in the DNA minor groove, the water bridge, for various DNA sequences to show that the water-bridge lifetime varies from 1 to ~300ps in a sequence-dependent manner. We find that it follows 1/k(V(step))P(m), where P(m) and V(step) are two crucial factors, namely the probability of forming a specific hydrogen bond in which more than one donor atom participates, and the structural fluctuation of DNA, respectively. This relationship provides a picture of the water kinetics with atomistic detail and shows that water dissociation occurs when a particular hydrogen-bonding pattern appears. The rate constant of water dissociation k can be described as a function of the structural fluctuations of DNA. This picture is consistent with the model of Laage and Hynes proposing that hydrogen-bond switching occurs when an unusual number of hydrogen bonds are formed. The two new factors suggested here are discussed in the context of the surface's geometry and electrostatic nature, which were previously proposed as the determinants of water lifetimes.

  14. A quantum molecular dynamics study of aqueous solvation dynamics

    Science.gov (United States)

    Videla, Pablo E.; Rossky, Peter J.; Laria, D.

    2013-10-01

    Ring polymer molecular dynamics experiments have been carried out to examine effects derived from nuclear quantum fluctuations at ambient conditions on equilibrium and non-equilibrium dynamical characteristics of charge solvation by a popular simple, rigid, water model, SPC/E, and for a more recent, and flexible, q-TIP4P/F model, to examine the generality of conclusions. In particular, we have recorded the relaxation of the solvent energy gap following instantaneous, ±e charge jumps in an initially uncharged Lennard-Jones-like solute. In both charge cases, quantum effects are reflected in sharper decays at the initial stages of the relaxation, which produce up to a ˜20% reduction in the characteristic timescales describing the solvation processes. For anionic solvation, the magnitude of polarization fluctuations controlling the extent of the water proton localization in the first solvation shell is somewhat more marked than for cations, bringing the quantum solvation process closer to the classical case. Effects on the solvation response from the explicit incorporation of flexibility in the water Hamiltonian are also examined. Predictions from linear response theories for the overall relaxation profile and for the corresponding characteristic timescales are reasonably accurate for the solvation of cations, whereas we find that they are much less satisfactory for the anionic case.

  15. Dynamic Wetting on Graphene-Coated Surface: Molecular Dynamics Investigation

    Science.gov (United States)

    Hung, Shih-Wei; Shiomi, Junichiro

    2015-11-01

    Wettability of graphene-coated surface gained significant attention recently due to discussion on the ``transparency'' (whether the wetting characteristics follow that of graphene or the underlying surface) and practical applications of graphene. In terms of static contact angle, the wettability of graphene-coated surfaces have been widely studied by experiments, simulations, and theory in recent years. However, the studies of dynamic wetting on graphene-coated surfaces are limited. In the present study, molecular dynamics simulation was performed to study the dynamic wetting of water droplet on graphene-coated surfaces from a microscopic point of view. The results show that the degree of similarity between the spreading behavior on graphene-coated surface and that on pure graphene (or that on the underlying surface) depends on time, i.e. how nonequilibrium the interface dynamics is. We also found that this feature can be altered by introducing defects into graphene. The work is partially supported by Grant-in-Aid for JSPS Fellows 26-04364 and JST CREST.

  16. Programming an interpreter using molecular dynamics

    OpenAIRE

    2008-01-01

    PGA (ProGram Algebra) is an algebra of programs which concerns programs in their simplest form: sequences of instructions. Molecular dynamics is a simple model of computation developed in the setting of \\PGA, which bears on the use of dynamic data structures in programming. We consider the programming of an interpreter for a program notation that is close to existing assembly languages using PGA with the primitives of molecular dynamics as basic instructions. It happens that, although primari...

  17. Programming an Interpreter Using Molecular Dynamics

    OpenAIRE

    2007-01-01

    PGA (ProGram Algebra) is an algebra of programs which concerns programs in their simplest form: sequences of instructions. Molecular dynamics is a simple model of computation developed in the setting of PGA, which bears on the use of dynamic data structures in programming.We consider the programming of an interpreter for a program notation that is close to existing assembly languages using PGA with the primitives of molecular dynamics as basic instructions. It happens that, although primarily...

  18. Amniotic fluid water dynamics.

    Science.gov (United States)

    Beall, M H; van den Wijngaard, J P H M; van Gemert, M J C; Ross, M G

    2007-01-01

    Water arrives in the mammalian gestation from the maternal circulation across the placenta. It then circulates between the fetal water compartments, including the fetal body compartments, the placenta and the amniotic fluid. Amniotic fluid is created by the flow of fluid from the fetal lung and bladder. A major pathway for amniotic fluid resorption is fetal swallowing; however in many cases the amounts of fluid produced and absorbed do not balance. A second resorption pathway, the intramembranous pathway (across the amnion to the fetal circulation), has been proposed to explain the maintenance of normal amniotic fluid volume. Amniotic fluid volume is thus a function both of the amount of water transferred to the gestation across the placental membrane, and the flux of water across the amnion. Membrane water flux is a function of the water permeability of the membrane; available data suggests that the amnion is the structure limiting intramembranous water flow. In the placenta, the syncytiotrophoblast is likely to be responsible for limiting water flow across the placenta. In human tissues, placental trophoblast membrane permeability increases with gestational age, suggesting a mechanism for the increased water flow necessary in late gestation. Membrane water flow can be driven by both hydrostatic and osmotic forces. Changes in both osmotic/oncotic and hydrostatic forces in the placenta my alter maternal-fetal water flow. A normal amniotic fluid volume is critical for normal fetal growth and development. The study of amniotic fluid volume regulation may yield important insights into the mechanisms used by the fetus to maintain water homeostasis. Knowledge of these mechanisms may allow novel treatments for amniotic fluid volume abnormalities with resultant improvement in clinical outcome.

  19. Thermodynamics and dynamics of supercooled water

    Science.gov (United States)

    Mazza, Marco G.

    This thesis employs methods of statistical mechanics and numerical simulations to study some aspects of the thermodynamic and dynamic behavior of liquid water. As liquid water is cooled down into the supercooled state, some regions of the sample show correlated molecular motion. Previously, only the translational motion has been the object of investigation. Given the importance of orientational dynamics for water, a question that naturally arises is whether the rotational molecular motion also shows heterogeneous dynamics. We show that the most rotationally mobile molecules tend to form clusters, "rotational heterogeneities", and we study their dependence upon observation time and temperature. Further, we show evidence that molecules belonging to dynamic heterogeneities are involved in bifurcated bonds. Since the presence of dynamic heterogeneities is increasingly important as the temperature is lowered, one would expect a signature of this phenomenon in dynamical quantities. We study the effect of dynamic heterogeneities on the origin of the breakdown of the Stokes--- Einstein and Stokes---Einstein---Debye relations for water. These relations link the diffusivity to temperature and viscosity. We study the separation of time scales of dynamic heterogeneities and the diffusive regime. We also consider different sets of mobility, slowest and fastest, for both translational and rotational heterogeneities. A long-standing problem in biology is the seemingly universal loss of biological activity of all biomolecules, a phenomenon termed the "protein glass transition". We explore the connection between the hypothesized liquid-liquid phase transition of water, and the protein glass transition. We find that the protein glass transition coincides with the crossing of the Widom line of hydration water. Many different scenarios have been proposed to rationalize water's thermodynamic anomalies. We study a tell model for water using the Wolff' cluster algorithm, which permits

  20. Origin of Asymmetric Solvation Effects for Ions in Water and Organic Solvents Investigated Using Molecular Dynamics Simulations: The Swain Acity-Basity Scale Revisited.

    Science.gov (United States)

    Reif, Maria M; Hünenberger, Philippe H

    2016-08-25

    The asymmetric solvation of ions can be defined as the tendency of a solvent to preferentially solvate anions over cations or cations over anions, at identical ionic charge magnitudes and effective sizes. Taking water as a reference, these effects are quantified experimentally for many solvents by the relative acity (A) and basity (B) parameters of the Swain scale. The goal of the present study is to investigate the asymmetric solvation of ions using molecular dynamics simulations, and to connect the results to this empirical scale. To this purpose, the charging free energies of alkali and halide ions, and of their hypothetical oppositely charged counterparts, are calculated in a variety of solvents. In a first set of calculations, artificial solvent models are considered that present either a charge or a shape asymmetry at the molecular level. The solvation asymmetry, probed by the difference in charging free energy between the two oppositely charged ions, is found to encompass a term quadratic in the ion charge, related to the different solvation structures around the anion and cation, and a term linear in the ion charge, related to the solvation structure around the uncharged ion-sized cavity. For these simple solvent models, the two terms are systematically counteracting each other, and it is argued that only the quadratic term should be retained when comparing the results of simulations involving physical solvents to experimental data. In a second set of calculations, 16 physical solvents are considered. The theoretical estimates for the acity A are found to correlate very well with the Swain parameters, whereas the correlation for B is very poor. Based on this observation, the Swain scale is reformulated into a new scale involving an asymmetry parameter Σ, positive for acitic solvents and negative for basitic ones, and a polarity parameter Π. This revised scale has the same predictive power as the original scale, but it characterizes asymmetry in an

  1. Nanodrop contact angles from molecular dynamics simulations

    Science.gov (United States)

    Ravipati, Srikanth; Aymard, Benjamin; Yatsyshin, Petr; Galindo, Amparo; Kalliadasis, Serafim

    2016-11-01

    The contact angle between three phases being in thermodynamic equilibrium is highly sensitive to the nature of the intermolecular forces as well as to various fluctuation effects. Determining the Young contact angle of a sessile drop sitting on a substrate from molecular dynamics (MD) simulations is a highly non-trivial task. Most commonly employed methods for finding droplet contact angles from MD simulation data either require large numbers of particles or are system-dependent. We propose a systematic geometry based methodology for extracting the contact angle from simulated sessile droplets by analysing an appropriately coarse-grained density field. To demonstrate the method, we consider Lennard-Jones (LJ) and SPC/E water nanodroplets of different sizes sitting on planar LJ walls. Our results are in good agreement with Young contact angle values computed employing test-area perturbation method.

  2. Thermally driven molecular linear motors - A molecular dynamics study

    DEFF Research Database (Denmark)

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

    2009-01-01

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

  3. Dynamic Combinatorial Libraries of Disulfide Cages in Water

    NARCIS (Netherlands)

    West, Kevin R.; Bake, Kyle D.; Otto, Sijbren

    2005-01-01

    Dynamic combinatorial libraries (DCLs) containing water-soluble disulfide-linked cages (alongside macrocyclic structures) have been generated and characterized. Unlike most other strategies for generating molecular cages, the structures are held together by covalent bonds, which are formed under

  4. Molecular Modeling of Enzyme Dynamics Towards Understanding Solvent Effects

    DEFF Research Database (Denmark)

    Wedberg, Nils Hejle Rasmus Ingemar

    This thesis describes the development of a molecular simulation methodology to study properties of enzymes in non-aqueous media at fixed thermodynamic water activities. The methodology is applied in a molecular dynamics study of the industrially important enzyme Candida antarctica lipase B (CALB...... integration, while for small systems, it seems to be even better. The method is applied to compute the excess Gibbs energy of the mixtures of water and organic solvents used in the simulations of CALB. This allows to determine the water activity of the simulated systems and thus to compare protein properties......), BMC Struct. Biol., 8) and the approach to fix the water activity which often is used in experimental studies. The water activity is shown to have a profound effect on the structure and dynamics of CALB. Conformational flexibility, for instance, increases with increasing hydration in acetone, t...

  5. Modulating weak interactions for molecular recognition: a dynamic combinatorial analysis for assessing the contribution of electrostatics to the stability of CH-π bonds in water.

    Science.gov (United States)

    Jiménez-Moreno, Ester; Gómez, Ana M; Bastida, Agatha; Corzana, Francisco; Jiménez-Oses, Gonzalo; Jiménez-Barbero, Jesús; Asensio, Juan Luis

    2015-03-27

    Electrostatic and charge-transfer contributions to CH-π complexes can be modulated by attaching electron-withdrawing substituents to the carbon atom. While clearly stabilizing in the gas phase, the outcome of this chemical modification in water is more difficult to predict. Herein we provide a definitive and quantitative answer to this question employing a simple strategy based on dynamic combinatorial chemistry.

  6. MOLECULAR DYNAMIC SIMULATION OF PEPTIDE POLYELECTROLYTES

    Directory of Open Access Journals (Sweden)

    I. M. Neelov

    2014-07-01

    Full Text Available The paper deals with investigation of the conformational properties of some charged homopolypeptides in dilute aqueous solutions by computer simulation. A method of molecular dynamics for the full-atomic models of polyaspartic acid and polylysine with explicit account of water and counter-ions is used for this purpose. For systems containing these polypeptides we calculated time trajectories and the size, shape, distribution functions and time correlation functions of inertia radius and the distances between the ends of peptide chains. We have also calculated the solvatation characteristics of considered polyelectrolytes. We have found out that polyaspartic acid in dilute aqueous solution has more compact structure and more spherical shape than polylysine. We have shown that these differences are due to different interaction between the polypeptides and water molecules (in particular, the quality and quantity of hydrogen bonds formed by these peptides with water, and the difference in an amount of ion pairs formed by the charged groups of the peptides and counter-ions. The obtained results should be taken into account for elaboration of new products based on the investigated peptides and their usage in various industrial and biomedical applications.

  7. Nanoscale deicing by molecular dynamics simulation

    Science.gov (United States)

    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

  8. Molecular Dynamics Simulation of Amyloid Beta Dimer Formation

    CERN Document Server

    Urbanc, B; Ding, F; Sammond, D; Khare, S; Buldyrev, S V; Stanley, H E; Dokholyan, N V

    2004-01-01

    Recent experiments with amyloid-beta (Abeta) peptide suggest that formation of toxic oligomers may be an important contribution to the onset of Alzheimer's disease. The toxicity of Abeta oligomers depends on their structure, which is governed by assembly dynamics. Due to limitations of current experimental techniques, a detailed knowledge of oligomer structure at the atomic level is missing. We introduce a molecular dynamics approach to study Abeta dimer formation: (1) we use discrete molecular dynamics simulations of a coarse-grained model to identify a variety of dimer conformations, and (2) we employ all-atom molecular mechanics simulations to estimate the thermodynamic stability of all dimer conformations. Our simulations of a coarse-grained Abeta peptide model predicts ten different planar beta-strand dimer conformations. We then estimate the free energies of all dimer conformations in all-atom molecular mechanics simulations with explicit water. We compare the free energies of Abeta(1-42) and Abeta(1-40...

  9. Dynamical processes in atomic and molecular physics

    CERN Document Server

    Ogurtsov, Gennadi

    2012-01-01

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

  10. Osmosis : a molecular dynamics computer simulation study

    Science.gov (United States)

    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..

  11. Ab initio Path Integral Molecular Dynamics Based on Fragment Molecular Orbital Method

    Science.gov (United States)

    Fujita, Takatoshi; Watanabe, Hirofumi; Tanaka, Shigenori

    2009-10-01

    We have developed an ab initio path integral molecular dynamics method based on the fragment molecular orbital method. This “FMO-PIMD” method can treat both nuclei and electrons quantum mechanically, and is useful to simulate large hydrogen-bonded systems with high accuracy. After a benchmark calculation for water monomer, water trimer and glycine pentamer have been studied using the FMO-PIMD method to investigate nuclear quantum effects on structure and molecular interactions. The applicability of the present approach is demonstrated through a number of test calculations.

  12. Molecular Dynamics Simulations of Simple Liquids

    Science.gov (United States)

    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.

  13. Molecular Dynamics Simulations of Simple Liquids

    Science.gov (United States)

    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.

  14. Molecular dynamics simulations of peptides on calcite surface

    OpenAIRE

    Yang, Mingjun; Rodger, Mark; Harding, John; Stipp, Susan S.L.

    2009-01-01

    Abstract A series of Molecular Dynamics (MD) simulations has been carried out to investigate the interaction between peptides and a calcite (1 0 -1 4) surface in water. A 16-amino acid and a 17-amino acid peptide have been built and three different configurations for each peptide are used as starting configurations. The dynamic behaviour of these peptides has been investigated by calculating their radii of gyration and distribution of dihedral angles. For comparison, the simulatio...

  15. Molecular dynamics studies of entangled polymer chains

    NARCIS (Netherlands)

    Bulacu, Monica Iulia

    2008-01-01

    The thesis presents three molecular dynamics studies of polymeric ensembles in which the chain entanglement plays the major role in the internal dynamics of the system. A coarse-grained model is used for representing the polymer chains as strings of beads connected by finite-extensible springs. In a

  16. A thread calculus with molecular dynamics

    NARCIS (Netherlands)

    Bergstra, J.A.; Middelburg, C.A.

    2010-01-01

    We present a theory of threads, interleaving of threads, and interaction between threads and services with features of molecular dynamics, a model of computation that bears on computations in which dynamic data structures are involved. Threads can interact with services of which the states consist o

  17. Programming an interpreter using molecular dynamics

    NARCIS (Netherlands)

    Bergstra, J.A.; Middelburg, C.A.

    2007-01-01

    PGA (ProGram Algebra) is an algebra of programs which concerns programs in their simplest form: sequences of instructions. Molecular dynamics is a simple model of computation developed in the setting of \\PGA, which bears on the use of dynamic data structures in programming. We consider the programmi

  18. Programming an interpreter using molecular dynamics

    NARCIS (Netherlands)

    Bergstra, J.A.; Middelburg, C.A.

    2007-01-01

    PGA (ProGram Algebra) is an algebra of programs which concerns programs in their simplest form: sequences of instructions. Molecular dynamics is a simple model of computation developed in the setting of \\PGA, which bears on the use of dynamic data structures in programming. We consider the

  19. Nanoscale deicing by molecular dynamics simulation.

    Science.gov (United States)

    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.

  20. Modeling hybrid perovskites by molecular dynamics.

    Science.gov (United States)

    Mattoni, Alessandro; Filippetti, Alessio; Caddeo, Claudia

    2017-02-01

    The topical review describes the recent progress in the modeling of hybrid perovskites by molecular dynamics simulations. Hybrid perovskites and in particular methylammonium lead halide (MAPI) have a tremendous technological relevance representing the fastest-advancing solar material to date. They also represent the paradigm of an organic-inorganic crystalline material with some conceptual peculiarities: an inorganic semiconductor for what concerns the electronic and absorption properties with a hybrid and solution processable organic-inorganic body. After briefly explaining the basic concepts of ab initio and classical molecular dynamics, the model potential recently developed for hybrid perovskites is described together with its physical motivation as a simple ionic model able to reproduce the main dynamical properties of the material. Advantages and limits of the two strategies (either ab initio or classical) are discussed in comparison with the time and length scales (from pico to microsecond scale) necessary to comprehensively study the relevant properties of hybrid perovskites from molecular reorientations to electrocaloric effects. The state-of-the-art of the molecular dynamics modeling of hybrid perovskites is reviewed by focusing on a selection of showcase applications of methylammonium lead halide: molecular cations disorder; temperature evolution of vibrations; thermally activated defects diffusion; thermal transport. We finally discuss the perspectives in the modeling of hybrid perovskites by molecular dynamics.

  1. Modeling hybrid perovskites by molecular dynamics

    Science.gov (United States)

    Mattoni, Alessandro; Filippetti, Alessio; Caddeo, Claudia

    2017-02-01

    The topical review describes the recent progress in the modeling of hybrid perovskites by molecular dynamics simulations. Hybrid perovskites and in particular methylammonium lead halide (MAPI) have a tremendous technological relevance representing the fastest-advancing solar material to date. They also represent the paradigm of an organic-inorganic crystalline material with some conceptual peculiarities: an inorganic semiconductor for what concerns the electronic and absorption properties with a hybrid and solution processable organic-inorganic body. After briefly explaining the basic concepts of ab initio and classical molecular dynamics, the model potential recently developed for hybrid perovskites is described together with its physical motivation as a simple ionic model able to reproduce the main dynamical properties of the material. Advantages and limits of the two strategies (either ab initio or classical) are discussed in comparison with the time and length scales (from pico to microsecond scale) necessary to comprehensively study the relevant properties of hybrid perovskites from molecular reorientations to electrocaloric effects. The state-of-the-art of the molecular dynamics modeling of hybrid perovskites is reviewed by focusing on a selection of showcase applications of methylammonium lead halide: molecular cations disorder; temperature evolution of vibrations; thermally activated defects diffusion; thermal transport. We finally discuss the perspectives in the modeling of hybrid perovskites by molecular dynamics.

  2. Molecular Dynamics Studies of Matrix Metalloproteases.

    Science.gov (United States)

    Díaz, Natalia; Suárez, Dimas

    2017-01-01

    Matrix metalloproteases are multidomain enzymes with a remarkable proteolytic activity located in the extracellular environment. Their catalytic activity and structural properties have been intensively studied during the last few decades using both experimental and theoretical approaches, but many open questions still remain. Extensive molecular dynamics simulations enable the sampling of the configurational space of a molecular system, thus contributing to the characterization of the structure, dynamics, and ligand binding properties of a particular MMP. Based on previous computational experience, we provide in this chapter technical and methodological guidelines that may be useful to and stimulate other researchers to perform molecular dynamics simulations to help address unresolved questions concerning the molecular mode of action of MMPs.

  3. Dynamics of hydrogen bonds in water and consequences for the unusual behaviour of supercooled water

    Indian Academy of Sciences (India)

    José Teixeira

    2008-10-01

    The dynamics of liquid water is evaluated by the coherent quasi-elastic scattering at two different momentum transfers, in order to discriminate hydrogen bond life-time from molecular dynamics. The results indicate a possible issue for the puzzle of the behaviour of supercooled water.

  4. Dynamic molecular crystals with switchable physical properties.

    Science.gov (United States)

    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.

  5. Self-assembling, reactivity and molecular dynamics of fullerenol nanoparticles.

    Science.gov (United States)

    Vraneš, Milan; Borišev, Ivana; Tot, Aleksandar; Armaković, Stevan; Armaković, Sanja; Jović, Danica; Gadžurić, Slobodan; Djordjevic, Aleksandar

    2016-12-21

    In this work structuring of water and insight into intermolecular interactions between water and fullerenol are studied throughout the process of forming nanoagglomerates at different temperatures applying both experimental and computational approaches. The obtained fullerenol nanoparticles (FNPs) are firstly characterized using dynamic light scattering, atomic force microscopy and transmission electron microscopy. The density, electrical conductivity and dynamic viscosity of aqueous fullerenol solutions are measured in the temperature range of 293.15 to 315.15 K. From the experimental density results other important thermodynamic values, such as apparent molar volumes and the partial molar volumes of water and fullerenol, are also calculated. To support the conclusion derived from the experimental density and calculated volumetric parameters, and to better understand the nature of the interactions with water, molecular dynamics simulations and radial distribution functions are also employed.

  6. Ice Formation on Kaolinite: Insights from Molecular Dynamics Simulations

    CERN Document Server

    Sosso, Gabriele C; Zen, Andrea; Pedevilla, Philipp; Michaelides, Angelos

    2016-01-01

    The formation of ice affects many aspects of our everyday life as well as technologies such as cryotherapy and cryopreservation. Foreign substances almost always aid water freezing through heterogeneous ice nucleation, but the molecular details of this process remain largely unknown. In fact, insight into the microscopic mechanism of ice formation on different substrates is difficult to obtain even via state-of-the-art experimental techniques. At the same time, atomistic simulations of heterogeneous ice nucleation frequently face extraordinary challenges due to the complexity of the water-substrate interaction and the long timescales that characterize nucleation events. Here, we have investigated several aspects of molecular dynamics simulations of heterogeneous ice nucleation considering as a prototypical ice nucleating material the clay mineral kaolinite, which is of relevance in atmospheric science. We show via seeded molecular dynamics simulations that ice nucleation on the hydroxylated (001) face of kaol...

  7. Random Matrix Theory in molecular dynamics analysis.

    Science.gov (United States)

    Palese, Luigi Leonardo

    2015-01-01

    It is well known that, in some situations, principal component analysis (PCA) carried out on molecular dynamics data results in the appearance of cosine-shaped low index projections. Because this is reminiscent of the results obtained by performing PCA on a multidimensional Brownian dynamics, it has been suggested that short-time protein dynamics is essentially nothing more than a noisy signal. Here we use Random Matrix Theory to analyze a series of short-time molecular dynamics experiments which are specifically designed to be simulations with high cosine content. We use as a model system the protein apoCox17, a mitochondrial copper chaperone. Spectral analysis on correlation matrices allows to easily differentiate random correlations, simply deriving from the finite length of the process, from non-random signals reflecting the intrinsic system properties. Our results clearly show that protein dynamics is not really Brownian also in presence of the cosine-shaped low index projections on principal axes.

  8. Exciton dynamics in molecular aggregates

    NARCIS (Netherlands)

    Augulis, R.; Pugžlys, A.; Loosdrecht, P.H.M. van; Pugzlys, A

    2006-01-01

    The fundamental aspects of exciton dynamics in double-wall cylindrical aggregates of cyanine dyes are studied by means of frequency resolved femtosecond pump-probe spectroscopy. The collective excitations of the aggregates, resulting from intermolecular dipole-dipole interactions have the characteri

  9. Exciton dynamics in molecular aggregates

    NARCIS (Netherlands)

    Augulis, R.; Pugžlys, A.; Loosdrecht, P.H.M. van; Pugzlys, A

    2006-01-01

    The fundamental aspects of exciton dynamics in double-wall cylindrical aggregates of cyanine dyes are studied by means of frequency resolved femtosecond pump-probe spectroscopy. The collective excitations of the aggregates, resulting from intermolecular dipole-dipole interactions have the

  10. Molecular dynamics using quasielastic neutron scattering

    CERN Document Server

    Mitra, S

    2003-01-01

    Quasielastic neutron scattering (QENS) technique is well suited to study the molecular motions (rotations and translations) in solids or liquids. It offers a unique possibility of analysing spatial dimensions of atomic or molecular processes in their development over time. We describe here some of the systems studied using the QENS spectrometer, designed, developed and commissioned at Dhruva reactor in Trombay. We have studied a variety of systems to investigate the molecular motion, for example, simple molecular solids, molecules adsorbed in confined medium like porous systems or zeolites, monolayer-protected nano-sized metal clusters, water in Portland cement as it cures with time, etc. (author)

  11. Liouville-von Neumann molecular dynamics

    Science.gov (United States)

    Jakowski, Jacek; Morokuma, Keiji

    2009-06-01

    We present a novel first principles molecular dynamics scheme, called Liouville-von Neumann molecular dynamics, based on Liouville-von Neumann equation for density matrices propagation and Magnus expansion of the time-evolution operator. The scheme combines formally accurate quantum propagation of electrons represented via density matrices and a classical propagation of nuclei. The method requires a few iterations per each time step where the Fock operator is formed and von Neumann equation is integrated. The algorithm (a) is free of constraint and fictitious parameters, (b) avoids diagonalization of the Fock operator, and (c) can be used in the case of fractional occupation as in metallic systems. The algorithm is very stable, and has a very good conservation of energy even in cases when a good quality conventional Born-Oppenheimer molecular dynamics trajectories is difficult to obtain. Test simulations include initial phase of fullerene formation from gaseous C2 and retinal system.

  12. Advances in molecular vibrations and collision dynamics molecular clusters

    CERN Document Server

    Bacic, Zatko

    1998-01-01

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

  13. Scalable Molecular Dynamics for Large Biomolecular Systems

    Directory of Open Access Journals (Sweden)

    Robert K. Brunner

    2000-01-01

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

  14. Theory and application of quantum molecular dynamics

    CERN Document Server

    Zeng Hui Zhang, John

    1999-01-01

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

  15. Molecular Biodynamers: Dynamic Covalent Analogues of Biopolymers

    Science.gov (United States)

    2017-01-01

    Conspectus Constitutional dynamic chemistry (CDC) features the use of reversible linkages at both molecular and supramolecular levels, including reversible covalent bonds (dynamic covalent chemistry, DCC) and noncovalent interactions (dynamic noncovalent chemistry, DNCC). Due to its inherent reversibility and stimuli-responsiveness, CDC has been widely utilized as a powerful tool for the screening of bioactive compounds, the exploitation of receptors or substrates driven by molecular recognition, and the fabrication of constitutionally dynamic materials. Implementation of CDC in biopolymer science leads to the generation of constitutionally dynamic analogues of biopolymers, biodynamers, at the molecular level (molecular biodynamers) through DCC or at the supramolecular level (supramolecular biodynamers) via DNCC. Therefore, biodynamers are prepared by reversible covalent polymerization or noncovalent polyassociation of biorelevant monomers. In particular, molecular biodynamers, biodynamers of the covalent type whose monomeric units are connected by reversible covalent bonds, are generated by reversible polymerization of bio-based monomers and can be seen as a combination of biopolymers with DCC. Owing to the reversible covalent bonds used in DCC, molecular biodynamers can undergo continuous and spontaneous constitutional modifications via incorporation/decorporation and exchange of biorelevant monomers in response to internal or external stimuli. As a result, they behave as adaptive materials with novel properties, such as self-healing, stimuli-responsiveness, and tunable mechanical and optical character. More specifically, molecular biodynamers combine the biorelevant characters (e.g., biocompatibility, biodegradability, biofunctionality) of bioactive monomers with the dynamic features of reversible covalent bonds (e.g., changeable, tunable, controllable, self-healing, and stimuli-responsive capacities), to realize synergistic properties in one system. In addition

  16. Molecular Biodynamers: Dynamic Covalent Analogues of Biopolymers.

    Science.gov (United States)

    Liu, Yun; Lehn, Jean-Marie; Hirsch, Anna K H

    2017-02-21

    Constitutional dynamic chemistry (CDC) features the use of reversible linkages at both molecular and supramolecular levels, including reversible covalent bonds (dynamic covalent chemistry, DCC) and noncovalent interactions (dynamic noncovalent chemistry, DNCC). Due to its inherent reversibility and stimuli-responsiveness, CDC has been widely utilized as a powerful tool for the screening of bioactive compounds, the exploitation of receptors or substrates driven by molecular recognition, and the fabrication of constitutionally dynamic materials. Implementation of CDC in biopolymer science leads to the generation of constitutionally dynamic analogues of biopolymers, biodynamers, at the molecular level (molecular biodynamers) through DCC or at the supramolecular level (supramolecular biodynamers) via DNCC. Therefore, biodynamers are prepared by reversible covalent polymerization or noncovalent polyassociation of biorelevant monomers. In particular, molecular biodynamers, biodynamers of the covalent type whose monomeric units are connected by reversible covalent bonds, are generated by reversible polymerization of bio-based monomers and can be seen as a combination of biopolymers with DCC. Owing to the reversible covalent bonds used in DCC, molecular biodynamers can undergo continuous and spontaneous constitutional modifications via incorporation/decorporation and exchange of biorelevant monomers in response to internal or external stimuli. As a result, they behave as adaptive materials with novel properties, such as self-healing, stimuli-responsiveness, and tunable mechanical and optical character. More specifically, molecular biodynamers combine the biorelevant characters (e.g., biocompatibility, biodegradability, biofunctionality) of bioactive monomers with the dynamic features of reversible covalent bonds (e.g., changeable, tunable, controllable, self-healing, and stimuli-responsive capacities), to realize synergistic properties in one system. In addition, molecular

  17. Molecular Scale Dynamics of Large Ring Polymers

    Science.gov (United States)

    Gooßen, S.; Brás, A. R.; Krutyeva, M.; Sharp, M.; Falus, P.; Feoktystov, A.; Gasser, U.; Pyckhout-Hintzen, W.; Wischnewski, A.; Richter, D.

    2014-10-01

    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.

  18. Molecular dynamics model of dimethyl ether

    Energy Technology Data Exchange (ETDEWEB)

    Lin, B.; Halley, W.J. [Univ. of Minnesota, Minneapolis, MN (United States)

    1995-11-02

    We report a molecular dynamics model of the monomeric liquid dimethyl ether. The united atom approach is used to treat CH{sub 3} groups as point source centers. Partial charges are derived from the experimental dipole moment. Harmonic force constants are used for intramolecular interactions, and their values are so chosen that the model`s fundamental frequencies agree with experimental results. Because we are interested in solvation properties, the model contains flexible molecules, allowing molecular distortion and internal dynamical quantities. We report radial distribution functions and the static structure factors as well as some dynamical quantities such as the dynamical structure factor, infrared absorption, and Raman scattering spectra. Calculated results agree reasonably well with experimental and other simulation results. 25 refs., 8 figs., 1 tab.

  19. Efficient compression of molecular dynamics trajectory files.

    Science.gov (United States)

    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.

  20. Water and Molecular Transport across Nanopores in Monolayer Graphene Membranes

    Science.gov (United States)

    Jang, Doojoon; O'Hern, Sean; Kidambi, Piran; Boutilier, Michael; Song, Yi; Idrobo, Juan-Carlos; Kong, Jing; Laoui, Tahar; Karnik, Rohit

    2015-11-01

    Graphene's atomic thickness and high tensile strength allow it to outstand as backbone material for next-generation high flux separation membrane. Molecular dynamics simulations predicted that a single-layer graphene membrane could exhibit high permeability and selectivity for water over ions/molecules, qualifying as novel water desalination membranes. However, experimental investigation of water and molecular transport across graphene nanopores had remained barely explored due to the presence of intrinsic defects and tears in graphene. We introduce two-step methods to seal leakage across centimeter scale single-layer graphene membranes create sub-nanometer pores using ion irradiation and oxidative etching. Pore creation parameters were varied to explore the effects of created pore structures on water and molecular transport driven by forward osmosis. The results demonstrate the potential of nanoporous graphene as a reliable platform for high flux nanofiltration membranes.

  1. Neutron Star Crust and Molecular Dynamics Simulation

    CERN Document Server

    Horowitz, C J; Schneider, A; Berry, D K

    2011-01-01

    In this book chapter we review plasma crystals in the laboratory, in the interior of white dwarf stars, and in the crust of neutron stars. We describe a molecular dynamics formalism and show results for many neutron star crust properties including phase separation upon freezing, diffusion, breaking strain, shear viscosity and dynamics response of nuclear pasta. We end with a summary and discuss open questions and challenges for the future.

  2. Dynamics and structure of water-bitumen mixtures

    DEFF Research Database (Denmark)

    Lemarchand, Claire; Greenfield, Michael L.; Hansen, Jesper Schmidt

    2016-01-01

    Systems of Cooee bitumen and water up to 4% mass are studied by molecular dynamics simulations. The cohesive energy density of the system is shown to decrease with an increasing water content. This decrease is due mainly to an increase in the interaction energy which is not high enough to counter...

  3. Hydrocarbons depending on the chain length and head group adopt different conformations within a water-soluble nanocapsule: 1H NMR and molecular dynamics studies.

    Science.gov (United States)

    Choudhury, Rajib; Barman, Arghya; Prabhakar, Rajeev; Ramamurthy, V

    2013-01-10

    In this study we have examined the conformational preference of phenyl-substituted hydrocarbons (alkanes, alkenes, and alkynes) of different chain lengths included within a confined space provided by a molecular capsule made of two host cavitands known by the trivial name "octa acid" (OA). One- and two-dimensional (1)H NMR experiments and molecular dynamics (MD) simulations were employed to probe the location and conformation of hydrocarbons within the OA capsule. In general, small hydrocarbons adopted a linear conformation while longer ones preferred a folded conformation. In addition, the extent of folding and the location of the end groups (methyl and phenyl) were dependent on the group (H(2)C-CH(2), HC═CH, and C≡C) adjacent to the phenyl group. In addition, the rotational mobility of the hydrocarbons within the capsule varied; for example, while phenylated alkanes tumbled freely, phenylated alkenes and alkynes resisted such a motion at room temperature. Combined NMR and MD simulation studies have confirmed that molecules could adopt conformations within confined spaces different from that in solution, opening opportunities to modulate chemical behavior of guest molecules.

  4. Water lubricates hydrogen-bonded molecular machines

    Science.gov (United States)

    Panman, Matthijs R.; Bakker, Bert H.; den Uyl, David; Kay, Euan R.; Leigh, David A.; Buma, Wybren Jan; Brouwer, Albert M.; Geenevasen, Jan A. J.; Woutersen, Sander

    2013-11-01

    The mechanical behaviour of molecular machines differs greatly from that of their macroscopic counterparts. This applies particularly when considering concepts such as friction and lubrication, which are key to optimizing the operation of macroscopic machinery. Here, using time-resolved vibrational spectroscopy and NMR-lineshape analysis, we show that for molecular machinery consisting of hydrogen-bonded components the relative motion of the components is accelerated strongly by adding small amounts of water. The translation of a macrocycle along a thread and the rotation of a molecular wheel around an axle both accelerate significantly on the addition of water, whereas other protic liquids have much weaker or opposite effects. We tentatively assign the superior accelerating effect of water to its ability to form a three-dimensional hydrogen-bond network between the moving parts of the molecular machine. These results may indicate a more general phenomenon that helps explain the function of water as the ‘lubricant of life’.

  5. Different aggregation dynamics of benzene-water mixtures.

    Science.gov (United States)

    Fu, Cen-Feng; Tian, Shan Xi

    2014-10-28

    All-atom molecular dynamics simulations for benzene-water mixtures are performed, aiming to explore the relationship between the microscopic structures and the thermodynamic properties, in particular, the transformation dynamics from the mutually soluble state to the phase-separated state. We find that the molecular aggregation of benzene in the water-rich mixture is distinctly different from that of water in the benzene-rich mixture. This aggregation difference is attributed to the different intermolecular interactions: the clustering of benzene molecules in the water-rich mixture is primarily driven by weak short-distance π-π interactions; while the formation of water clusters in the benzene-rich solution is triggered by long-range dipole-dipole electrostatic interactions. Moreover, the molecular aggregations show double-scaled features: firstly assembling in a quasi-plane at a low concentration, then bulking in three dimensions with an increase in concentration.

  6. Molecular dynamics simulation of impact test

    Energy Technology Data Exchange (ETDEWEB)

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

    1998-11-01

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

  7. Reaction dynamics in polyatomic molecular systems

    Energy Technology Data Exchange (ETDEWEB)

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

    1993-12-01

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

  8. Molecular dynamics modeling of structural battery components

    NARCIS (Netherlands)

    Verners, O.; Van Duin, A.C.T.; Wagemaker, M.; Simone, A.

    2015-01-01

    A crosslinked polymer based solid electrolyte prototype material –poly(propylene glycol) diacrylate– is studied using the reactive molecular dynamics force field ReaxFF. The focus of the study is the evaluation of the effects of equilibration and added plasticizer (ethylene carbonate) or anion compo

  9. Catalysis and communication in dynamic molecular networks

    NARCIS (Netherlands)

    Fanlo Virgos, Hugo

    2015-01-01

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

  10. Molecular Exchange Dynamics in Block Copolymer Micelles

    Science.gov (United States)

    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.

  11. Multiscale coupling of molecular dynamics and peridynamics

    Science.gov (United States)

    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.

  12. MDMovie: a molecular dynamics viewing tool.

    Science.gov (United States)

    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.

  13. Dynamics and Thermodynamics of Molecular Machines

    DEFF Research Database (Denmark)

    Golubeva, Natalia

    2014-01-01

    Molecular machines, or molecular motors, are small biophysical devices that perform a variety of essential metabolic processes such as DNA replication, protein synthesis and intracellular transport. Typically, these machines operate by converting chemical energy into motion and mechanical work. Due...... to their microscopic size, molecular motors are governed by principles fundamentally different from those describing the operation of man-made motors such as car engines. In this dissertation the dynamic and thermodynamic properties of molecular machines are studied using the tools of nonequilibrium statistical...... of the important trade-off between power output and efficiency. Steric motor-motor interactions are shown to play an important thermodynamic role by enhancing the EMP as compared to the noninteracting case. Remarkably, the enhancement occurs at biologically relevant parameters. Finally, a generic model of motor...

  14. Dynamical quenching of tunneling in molecular magnets

    Energy Technology Data Exchange (ETDEWEB)

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

    2015-12-15

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

  15. How Mg(2+) ion and water network affect the stability and structure of non-Watson-Crick base pairs in E. coli loop E of 5S rRNA: a molecular dynamics and reference interaction site model (RISM) study.

    Science.gov (United States)

    Shanker, Sudhanshu; Bandyopadhyay, Pradipta

    2017-08-01

    The non-Watson-Crick (non-WC) base pairs of Escherichia coli loop E of 5S rRNA are stabilized by Mg(2+) ions through water-mediated interaction. It is important to know the synergic role of Mg(2+) and the water network surrounding Mg(2+) in stabilizing the non-WC base pairs of RNA. For this purpose, free energy change of the system is calculated using molecular dynamics (MD) simulation as Mg(2+) is pulled from RNA, which causes disturbance of the water network. It was found that Mg(2+) remains hexahydrated unless it is close to or far from RNA. In the pentahydrated form, Mg(2+) interacts directly with RNA. Water network has been identified by two complimentary methods; MD followed by a density-based clustering algorithm and three-dimensional-reference interaction site model. These two methods gave similar results. Identification of water network around Mg(2+) and non-WC base pairs gives a clue to the strong effect of water network on the stability of this RNA. Based on sequence analysis of all Eubacteria 5s rRNA, we propose that hexahydrated Mg(2+) is an integral part of this RNA and geometry of base pairs surrounding it adjust to accommodate the [Formula: see text]. Overall the findings from this work can help in understanding the basis of the complex structure and stability of RNA with non-WC base pairs.

  16. Anomalous flow behavior in nanochannels: A molecular dynamics study

    Science.gov (United States)

    Murad, Sohail; Luo, Lin; Chu, Liang-Yin

    2010-06-01

    We report molecular dynamics simulations of flow of water in nanochannels with a range of surface wettability characteristics (hydrophobic to strongly hydrophilic) and driving forces (pressures). Our results show apparently anomalous behavior. At low pressures, the rate is higher in nanochannels with hydrophilic surfaces than that with hydrophobic surfaces; however, with high pressure driven flow we observe opposite trends. This apparently anomalous behavior can be explained on the basis of molecular thermodynamics and fluid mechanics considerations. Understanding such behavior is important in many nanofluidic devices such as nanoreactors, nanosensors, and nanochips that are increasingly being designed and used.

  17. Computationally Efficient Multiconfigurational Reactive Molecular Dynamics.

    Science.gov (United States)

    Yamashita, Takefumi; Peng, Yuxing; Knight, Chris; Voth, Gregory A

    2012-12-11

    It is a computationally demanding task to explicitly simulate the electronic degrees of freedom in a system to observe the chemical transformations of interest, while at the same time sampling the time and length scales required to converge statistical properties and thus reduce artifacts due to initial conditions, finite-size effects, and limited sampling. One solution that significantly reduces the computational expense consists of molecular models in which effective interactions between particles govern the dynamics of the system. If the interaction potentials in these models are developed to reproduce calculated properties from electronic structure calculations and/or ab initio molecular dynamics simulations, then one can calculate accurate properties at a fraction of the computational cost. Multiconfigurational algorithms model the system as a linear combination of several chemical bonding topologies to simulate chemical reactions, also sometimes referred to as "multistate". These algorithms typically utilize energy and force calculations already found in popular molecular dynamics software packages, thus facilitating their implementation without significant changes to the structure of the code. However, the evaluation of energies and forces for several bonding topologies per simulation step can lead to poor computational efficiency if redundancy is not efficiently removed, particularly with respect to the calculation of long-ranged Coulombic interactions. This paper presents accurate approximations (effective long-range interaction and resulting hybrid methods) and multiple-program parallelization strategies for the efficient calculation of electrostatic interactions in reactive molecular simulations.

  18. Animated molecular dynamics simulations of hydrated caesium-smectite interlayers

    Directory of Open Access Journals (Sweden)

    Sposito Garrison

    2002-09-01

    Full Text Available Computer animation of center of mass coordinates obtained from 800 ps molecular dynamics simulations of Cs-smectite hydrates (1/3 and 2/3 water monolayers provided information concerning the structure and dynamics of the interlayer region that could not be obtained through traditional simulation analysis methods. Cs+ formed inner sphere complexes with the mineral surface, and could be seen to jump from one attracting location near a layer charge site to the next, while water molecules were observed to migrate from the hydration shell of one ion to that of another. Neighboring ions maintained a partial hydration shell by sharing water molecules, such that a single water molecule hydrated two ions simultaneously for hundreds of picoseconds. Cs-montmorillonite hydrates featured the largest extent of this sharing interaction, because interlayer ions were able to inhabit positions near surface cavities as well as at their edges, close to oxygen triads. The greater positional freedom of Cs+ within the montmorillonite interlayer, a result of structural hydroxyl orientation and low tetrahedral charge, promoted the optimization of distances between cations and water molecules required for water sharing. Preference of Cs+ for locations near oxygen triads was observed within interlayer beidellite and hectorite. Water molecules also could be seen to interact directly with the mineral surface, entering its surface cavities to approach attracting charge sites and structural hydroxyls. With increasing water content, water molecules exhibited increased frequency and duration of both cavity habitation and water sharing interactions. Competition between Cs+ and water molecules for surface sites was evident. These important cooperative and competitive features of interlayer molecular behavior were uniquely revealed by animation of an otherwise highly complex simulation output.

  19. Dynamic assembly of molecularly imprinted polymer nanoparticles.

    Science.gov (United States)

    Gong, Haiyue; Hajizadeh, Solmaz; Jiang, Lingdong; Ma, Huiting; Ye, Lei

    2017-09-11

    Manipulation of specific binding and recycling of materials are two important aspects for practical applications of molecularly imprinted polymers. In this work, we developed a new approach to control the dynamic assembly of molecularly imprinted nanoparticles by surface functionalization. Molecularly imprinted polymer nanoparticles with a well-controlled core-shell structure were synthesized using precipitation polymerization. The specific binding sites were created in the core during the first step imprinting reaction. In the second polymerization step, epoxide groups were introduced into the particle shell to act asan intermediate linker to immobilize phenylboronic acids, as well as to introduce cis-diol structures on surface. The imprinted polymer nanoparticles modified with boronic acid and cis-diol structures maintained high molecular binding specificity, and the nanoparticles could be induced to form dynamic particle aggregation that responded to pH variation and chemical stimuli. The possibility of modulating molecular binding and nanoparticle assembly in a mutually independent fashion can be exploited in a number of applications where repeated use of precious nanoparticles is needed. Copyright © 2017 Elsevier Inc. All rights reserved.

  20. Molecular dynamics simulation of anionic clays containing glutamic acid

    Science.gov (United States)

    Xu, Qian; Ni, Zheming; Yao, Ping; Li, Yuan

    2010-08-01

    Supra-molecular structure of glutamic acid intercalated ZnAl layered double hydroxides (Glu-ZnAl-LDH) was modeled by molecular dynamics (MD) methods. Hydrogen bonding, hydration and swelling properties of Glu-LDH have been investigated. For Nw layers and anions. When A-W type H-bonds gradually reached a saturation state, water molecules continued to form hydrogen bonds with the hydroxyls of the layers. The L-W type H-bonds gradually substituted the L-A type H-bonds and Glu anions moved to the center of an interlayer and then separated with the layers. Last, a well-ordered structural water layer was formed on the surface hydroxyls of Glu-LDH. The lower releasing content of Glu-LDH maybe was influenced by the lower balance hydration energy and existence of L-A type H-bonds in high water content.

  1. Simulation study of water and sugar dynamics in supercooled mixtures

    Science.gov (United States)

    Molinero, Valeria; Cagin, Tahir; Goddard, William A.

    2003-03-01

    Water dynamics in concentrated carbohydrate solutions is of utmost importance in food and pharmaceutical technology, where low water mobility is desirable to slow down chemical degradation and preserve biomolecules. We have studied the microscopic mechanism of water diffusion in binary and polydisperse malto-oligosaccharides and water mixtures by means of molecular dynamics simulations. The computations were performed with a coarse grain model (M3B), derived from atomistic simulations of water and malto-oligosaccharides. The use of the M3B model permits simulations of the order of 0.1 microsecond, thus allowing us to explore water dynamics from the liquid to the deep supercooled regime. The dynamics of water confined in the sugar matrix is slowed down with respect to bulk water. We found that at low moisture content and low temperature, ranslational diffusion of water and glucose rotation proceed through a hopping-diffusion mechanism. Moreover, we found water mobility to be heterogeneous: there is a broad distribution of time scales for different water molecules in the mixtures. We discuss whether there is a relationship between the heterogeneous structure of these mixtures in the sub-nanometer scale and the heterogeneous dynamics of water molecules.

  2. Ab initio molecular orbital calculation considering the quantum mechanical effect of nuclei by path integral molecular dynamics

    Science.gov (United States)

    Shiga, Motoyuki; Tachikawa, Masanori; Miura, Shinichi

    2000-12-01

    We present an accurate calculational scheme for many-body systems composed of electrons and nuclei, by path integral molecular dynamics technique combined with the ab initio molecular orbital theory. Based upon the scheme, the simulation of a water molecule at room temperature is demonstrated, applying all-electron calculation at the Hartree-Fock level of theory.

  3. Molecular Dynamics Simulations and Empirical Observations on Soy Lecithin Liposome Preparation

    Directory of Open Access Journals (Sweden)

    Rini Dwiastuti

    2016-08-01

    Full Text Available Soy lecithin is a phospholipid often used in liposome formulations. Determination of water and phospholipid composition is one of the problems in the liposome formulation. This study is using molecular dynamics simulation and empirical observation in producing liposome preparations. Phospholipids 1,2-dilauroyl-sn-glycero-3-phosphoethanolamine (DLPE were objected in molecular dynamics simulations using Coarse Grained Molecular Dynamics (CGMD approaches. The result showed that the molecular dynamic simulations could be employed to predict the liposome size. The molecular dynamic simulations resulted in liposome size of 71.22 ± 2.54 nm, which was located within the range of the liposome size resulted from the empirical observations (95.99 ± 43.02 nm. Moreover, similar liposome forms were observed on both results of molecular dynamics simulations and empirical approaches.

  4. Atomic dynamics of alumina melt: A molecular dynamics simulation study

    Directory of Open Access Journals (Sweden)

    S.Jahn

    2008-03-01

    Full Text Available The atomic dynamics of Al2O3 melt are studied by molecular dynamics simulation. The particle interactions are described by an advanced ionic interaction model that includes polarization effects and ionic shape deformations. The model has been shown to reproduce accurately the static structure factors S(Q from neutron and x-ray diffraction and the dynamic structure factor S(Q,ω from inelastic x-ray scattering. Analysis of the partial dynamic structure factors shows inelastic features in the spectra up to momentum transfers, Q, close to the principal peaks of partial static structure factors. The broadening of the Brillouin line widths is discussed in terms of a frequency dependent viscosity η(ω.

  5. Open quantum system parameters from molecular dynamics

    CERN Document Server

    Wang, Xiaoqing; Wüster, Sebastian; Eisfeld, Alexander

    2015-01-01

    We extract the site energies and spectral densities of the Fenna-Matthews-Olson (FMO) pigment protein complex of green sulphur bacteria from simulations of molecular dynamics combined with energy gap calculations. Comparing four different combinations of methods, we investigate the origin of quantitative differences regarding site energies and spectral densities obtained previously in the literature. We find that different forcefields for molecular dynamics and varying local energy minima found by the structure relaxation yield significantly different results. Nevertheless, a picture averaged over these variations is in good agreement with experiments and some other theory results. Throughout, we discuss how vibrations external- or internal to the pigment molecules enter the extracted quantities differently and can be distinguished. Our results offer some guidance to set up more computationally intensive calculations for a precise determination of spectral densities in the future. These are required to determ...

  6. Molecular dynamics simulations of classical stopping power.

    Science.gov (United States)

    Grabowski, Paul E; Surh, Michael P; Richards, David F; Graziani, Frank R; Murillo, Michael S

    2013-11-22

    Molecular dynamics can provide very accurate tests of classical kinetic theory; for example, unambiguous comparisons can be made for classical particles interacting via a repulsive 1/r potential. The plasma stopping power problem, of great interest in its own right, provides an especially stringent test of a velocity-dependent transport property. We have performed large-scale (~10(4)-10(6) particles) molecular dynamics simulations of charged-particle stopping in a classical electron gas that span the weak to moderately strong intratarget coupling regimes. Projectile-target coupling is varied with projectile charge and velocity. Comparisons are made with disparate kinetic theories (both Boltzmann and Lenard-Balescu classes) and fully convergent theories to establish regimes of validity. We extend these various stopping models to improve agreement with the MD data and provide a useful fit to our results.

  7. Characterization of Rare Events in Molecular Dynamics

    Directory of Open Access Journals (Sweden)

    Carsten Hartmann

    2013-12-01

    Full Text Available A good deal of molecular dynamics simulations aims at predicting and quantifying rare events, such as the folding of a protein or a phase transition. Simulating rare events is often prohibitive, especially if the equations of motion are high-dimensional, as is the case in molecular dynamics. Various algorithms have been proposed for efficiently computing mean first passage times, transition rates or reaction pathways. This article surveys and discusses recent developments in the field of rare event simulation and outlines a new approach that combines ideas from optimal control and statistical mechanics. The optimal control approach described in detail resembles the use of Jarzynski’s equality for free energy calculations, but with an optimized protocol that speeds up the sampling, while (theoretically giving variance-free estimators of the rare events statistics. We illustrate the new approach with two numerical examples and discuss its relation to existing methods.

  8. 受限于碳纳米管中水分子微观结构的分子动力学模拟研究%Molecular Dynamics Study on Microscopic Structure of Water Molecules Confined in Carbon Nanotubes

    Institute of Scientific and Technical Information of China (English)

    刘华; 李春艳; 陈建超; 杨晓峰

    2011-01-01

    Molecular dynamics simulation were performed to study microscopic structure of water molecules confined in the different diameters of carbon nanotubes. Changing the temperature, the radial distribution function diagram of the water molecules confined in the carbon nanotubes was made. By doing the mean square displacement versus time graph of water molecules in carbon nanotubes, diffusion coefficient of water molecules in different diameters of carbon nanotubes was calculated with Einstein method, and it was compared with the diffusion coefficient of water molecules calculated by Knudsen diffusion.%利用分子动力学模拟研究受限于不同管径中水分子的微观结构,改变温度,做出受限水分子的径向分布函数图,并对比说明。通过做水分子在碳纳米管内的均方位移与时间关系图,利用Einstein法算出不同管径中水分子的扩散系数,与利用Knudsen扩散公式计算出的水分子的扩散系数进行比较。

  9. Molecular dynamics-based refinement of nanodiamond size measurements obtained with dynamic light scattering

    CERN Document Server

    Koniakhin, S V; Terterov, I N; Shvidchenko, A V; Eidelman, E D; Dubina, M V

    2016-01-01

    The determination of particle size by dynamic light scattering uses the Stokes-Einstein relation, which can break down for nanoscale objects. Here we employ a molecular dynamics simulation of fully solvated 1-5 nm carbon nanoparticles for the refinement of the experimental data obtained for nanodiamonds in water by using dynamic light scattering. We performed molecular dynamics simulations in differently sized boxes and calculated nanoparticles diffusion coefficients using the velocity autocorrelation function and mean-square displacement. We found that the predictions of the Stokes-Einstein relation are accurate for nanoparticles larger than 3 nm while for smaller nanoparticles the diffusion coefficient should be corrected and different boundary conditions should be taken into account.

  10. Ice formation on kaolinite: Insights from molecular dynamics simulations

    Science.gov (United States)

    Sosso, Gabriele C.; Tribello, Gareth A.; Zen, Andrea; Pedevilla, Philipp; Michaelides, Angelos

    2016-12-01

    The formation of ice affects many aspects of our everyday life as well as important technologies such as cryotherapy and cryopreservation. Foreign substances almost always aid water freezing through heterogeneous ice nucleation, but the molecular details of this process remain largely unknown. In fact, insight into the microscopic mechanism of ice formation on different substrates is difficult to obtain even if state-of-the-art experimental techniques are used. At the same time, atomistic simulations of heterogeneous ice nucleation frequently face extraordinary challenges due to the complexity of the water-substrate interaction and the long time scales that characterize nucleation events. Here, we have investigated several aspects of molecular dynamics simulations of heterogeneous ice nucleation considering as a prototypical ice nucleating material the clay mineral kaolinite, which is of relevance in atmospheric science. We show via seeded molecular dynamics simulations that ice nucleation on the hydroxylated (001) face of kaolinite proceeds exclusively via the formation of the hexagonal ice polytype. The critical nucleus size is two times smaller than that obtained for homogeneous nucleation at the same supercooling. Previous findings suggested that the flexibility of the kaolinite surface can alter the time scale for ice nucleation within molecular dynamics simulations. However, we here demonstrate that equally flexible (or non flexible) kaolinite surfaces can lead to very different outcomes in terms of ice formation, according to whether or not the surface relaxation of the clay is taken into account. We show that very small structural changes upon relaxation dramatically alter the ability of kaolinite to provide a template for the formation of a hexagonal overlayer of water molecules at the water-kaolinite interface, and that this relaxation therefore determines the nucleation ability of this mineral.

  11. Study of Nanowires Using Molecular Dynamics Simulations

    OpenAIRE

    Monk, Joshua D

    2007-01-01

    In this dissertation I present computational studies that focus on the unique characteristics of metallic nanowires. We generated virtual nanowires of nanocrystalline nickel (nc-Ni) and single crystalline silver (Ag) in order to investigate particular nanoscale effects. Three-dimensional atomistic molecular dynamics studies were performed for each sample using the super computer System X located at Virginia Tech. Thermal grain growth simulations were performed on 4 nm grain size nc-Ni by o...

  12. Molecular dynamics modelling of solidification in metals

    Energy Technology Data Exchange (ETDEWEB)

    Boercker, D.B.; Belak, J.; Glosli, J. [Lawrence Livermore National Lab., CA (United States)

    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.

  13. Molecular crowding and protein enzymatic dynamics.

    Science.gov (United States)

    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.

  14. Monoamine transporters: Insights from molecular dynamics simulations

    Directory of Open Access Journals (Sweden)

    Julie eGrouleff

    2015-10-01

    Full Text Available The human monoamine transporters facilitate the reuptake of the neurotransmitters serotonin, dopamine, and norepinephrine from the synaptic cleft. Imbalance in monoaminergic neurotransmission is linked to various diseases including major depression, attention deficit hyperactivity disorder, schizophrenia and Parkinson’s disease. Inhibition of the monoamine transporters is thus an important strategy for treatment of such diseases. The monoamine transporters are sodium-coupled transport proteins belonging to the neurotransmitter/Na+ symporter (NSS family, and the publication of the first high-resolution structure of a NSS family member, the bacterial leucine transporter LeuT, in 2005, proved to be a major stepping stone for understanding this family of transporters. Structural data allows for the use of computational methods to study the monoamine transporters, which in turn has led to a number of important discoveries. The process of substrate translocation across the membrane is an intrinsically dynamic process. Molecular dynamics simulations, which can provide atomistic details of molecular motion on ns to ms timescales, are therefore well-suited for studying transport processes. In this review, we outline how molecular dynamics simulations have provided insight into the large scale motions associated with transport of the neurotransmitters, as well as the presence of external and internal gates, the coupling between ion and substrate transport, and differences in the conformational changes induced by substrates and inhibitors.

  15. Bead-Fourier path integral molecular dynamics

    Science.gov (United States)

    Ivanov, Sergei D.; Lyubartsev, Alexander P.; Laaksonen, Aatto

    2003-06-01

    Molecular dynamics formulation of Bead-Fourier path integral method for simulation of quantum systems at finite temperatures is presented. Within this scheme, both the bead coordinates and Fourier coefficients, defining the path representing the quantum particle, are treated as generalized coordinates with corresponding generalized momenta and masses. Introduction of the Fourier harmonics together with the center-of-mass thermostating scheme is shown to remove the ergodicity problem, known to pose serious difficulties in standard path integral molecular dynamics simulations. The method is tested for quantum harmonic oscillator and hydrogen atom (Coulombic potential). The simulation results are compared with the exact analytical solutions available for both these systems. Convergence of the results with respect to the number of beads and Fourier harmonics is analyzed. It was shown that addition of a few Fourier harmonics already improves the simulation results substantially, even for a relatively small number of beads. The proposed Bead-Fourier path integral molecular dynamics is a reliable and efficient alternative to simulations of quantum systems.

  16. Monoamine transporters: insights from molecular dynamics simulations

    Science.gov (United States)

    Grouleff, Julie; Ladefoged, Lucy Kate; Koldsø, Heidi; Schiøtt, Birgit

    2015-01-01

    The human monoamine transporters (MATs) facilitate the reuptake of the neurotransmitters serotonin, dopamine, and norepinephrine from the synaptic cleft. Imbalance in monoaminergic neurotransmission is linked to various diseases including major depression, attention deficit hyperactivity disorder, schizophrenia, and Parkinson’s disease. Inhibition of the MATs is thus an important strategy for treatment of such diseases. The MATs are sodium-coupled transport proteins belonging to the neurotransmitter/Na+ symporter (NSS) family, and the publication of the first high-resolution structure of a NSS family member, the bacterial leucine transporter LeuT, in 2005, proved to be a major stepping stone for understanding this family of transporters. Structural data allows for the use of computational methods to study the MATs, which in turn has led to a number of important discoveries. The process of substrate translocation across the membrane is an intrinsically dynamic process. Molecular dynamics simulations, which can provide atomistic details of molecular motion on ns to ms timescales, are therefore well-suited for studying transport processes. In this review, we outline how molecular dynamics simulations have provided insight into the large scale motions associated with transport of the neurotransmitters, as well as the presence of external and internal gates, the coupling between ion and substrate transport, and differences in the conformational changes induced by substrates and inhibitors. PMID:26528185

  17. Nonequilibrium molecular dynamics theory, algorithms and applications

    CERN Document Server

    Todd, Billy D

    2017-01-01

    Written by two specialists with over twenty-five years of experience in the field, this valuable text presents a wide range of topics within the growing field of nonequilibrium molecular dynamics (NEMD). It introduces theories which are fundamental to the field - namely, nonequilibrium statistical mechanics and nonequilibrium thermodynamics - and provides state-of-the-art algorithms and advice for designing reliable NEMD code, as well as examining applications for both atomic and molecular fluids. It discusses homogenous and inhomogenous flows and pays considerable attention to highly confined fluids, such as nanofluidics. In addition to statistical mechanics and thermodynamics, the book covers the themes of temperature and thermodynamic fluxes and their computation, the theory and algorithms for homogenous shear and elongational flows, response theory and its applications, heat and mass transport algorithms, applications in molecular rheology, highly confined fluids (nanofluidics), the phenomenon of slip and...

  18. Control-volume representation of molecular dynamics.

    Science.gov (United States)

    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.

  19. Learning generative models of molecular dynamics.

    Science.gov (United States)

    Razavian, Narges Sharif; Kamisetty, Hetunandan; Langmead, Christopher J

    2012-01-01

    We introduce three algorithms for learning generative models of molecular structures from molecular dynamics simulations. The first algorithm learns a Bayesian-optimal undirected probabilistic model over user-specified covariates (e.g., fluctuations, distances, angles, etc). L1 regularization is used to ensure sparse models and thus reduce the risk of over-fitting the data. The topology of the resulting model reveals important couplings between different parts of the protein, thus aiding in the analysis of molecular motions. The generative nature of the model makes it well-suited to making predictions about the global effects of local structural changes (e.g., the binding of an allosteric regulator). Additionally, the model can be used to sample new conformations. The second algorithm learns a time-varying graphical model where the topology and parameters change smoothly along the trajectory, revealing the conformational sub-states. The last algorithm learns a Markov Chain over undirected graphical models which can be used to study and simulate kinetics. We demonstrate our algorithms on multiple molecular dynamics trajectories.

  20. Dynamic Maintenance and Visualization of Molecular Surfaces

    Energy Technology Data Exchange (ETDEWEB)

    Bajaj, C L; Pascucci, V; Shamir, A; Holt, R J; Netravali, A N

    2004-12-16

    Molecular surface computations are often necessary in order to perform synthetic drug design. A critical step in this process is the computation and update of an exact boundary representation for the molecular surface (e.g. the Lee-Richards surface). In this paper they introduce efficient techniques for computing a molecular surface boundary representation as a set of NURBS (non-uniform rational B-splines) patches. This representation introduces for molecules the same geometric data structure used in the solid modeling community and enables immediate access to a wide range of modeling operations and techniques. Furthermore, this allows the use of any general solid modeling or visualization system as a molecular modeling interface. However, using such a representation in a molecular modeling environment raises several efficiency and update constraints, especially in a dynamic setting. For example, changes in the probe radius result in both geometric and topological changes to the set of patches. The techniques provide the option of trading accuracy of the representation for the efficiency of the computation, while still tracking the changes in the set of patches. In particular, they discuss two main classes of dynamic updates: one that keeps the topology of the molecular configuration fixed, and a more complicated case where the topology may be updated continuously. In general the generated output surface is represented in a format that can be loaded into standard solid modeling systems. It can also be directly triangulated or rendered, possibly at different levels of resolution, by a standard graphics library such as OpenGL without any additional effort.

  1. Molecular Dynamics Simulations of Adhesion at Epoxy Interfaces

    Science.gov (United States)

    Frankland, Sarah-Jane V.; Clancy, Thomas C.; Hinkley, J. A.; Gates. T. S.

    2008-01-01

    The effect of moisture on adhesives used in aerospace applications can be modeled with chemically specific techniques such as molecular dynamics simulation. In the present study, the surface energy and work of adhesion are calculated for epoxy surfaces and interfaces, respectively, by using molecular dynamics simulation. Modifications are made to current theory to calculate the work of adhesion at the epoxy-epoxy interface with and without water. Quantitative agreement with experimental values is obtained for the surface energy and work of adhesion at the interface without water. The work of adhesion agrees qualitatively with the experimental values for the interface with water: the magnitude is reduced 15% with respect to the value for the interface without water. A variation of 26% in the magnitude is observed depending on the water configuration at a concentration of 1.6 wt%. The methods and modifications to the method that are employed to obtain these values are expected to be applicable for other epoxy adhesives to determine the effects of moisture uptake on their work of adhesion.

  2. Specific Electrostatic Molecular Recognition in Water

    DEFF Research Database (Denmark)

    Li, Ming; Hoeck, Casper; Schoffelen, Sanne;

    2016-01-01

    -bead binding assay and by 2D NMR spectroscopy. Molecular dynamics (MD) studies revealed a putative mode of interaction for this unusual electrostatic binding event. High binding specificity occurred through a combination of topological matching and electrostatic and hydrogen-bond complementarities. From MD...

  3. Molecular dynamics simulations of magnetized dusty plasmas

    Science.gov (United States)

    Piel, Alexander; Reichstein, Torben; Wilms, Jochen

    2012-10-01

    The combination of the electric field that confines a dust cloud with a static magnetic field generally leads to a rotation of the dust cloud. In weak magnetic fields, the Hall component of the ion flow exerts a drag force that sets the dust in rotation. We have performed detailed molecular-dynamics simulations of the dynamics of torus-shaped dust clouds in anodic plasmas. The stationary flow [1] is characterized by a shell structure in the laminar dust flow and by the spontaneous formation of a shear-flow around a stationary vortex. Here we present new results on dynamic phenomena, among them fluctuations due to a Kelvin-Helmholtz instability in the shear-flow. The simulations are compared with experimental results. [4pt] [1] T. Reichstein, A. Piel, Phys. Plasmas 18, 083705 (2011)

  4. 分子动力学模拟超临界水微观结构及自扩散系数%Microstructure and self-diffusion coefficient of supercritical water by molecular dynamics simulation

    Institute of Scientific and Technical Information of China (English)

    张乃强; 徐鸿; 白杨

    2011-01-01

    By using molecular dynamics simulation with COMPASS force field, microstructure and self-diffusion coefficient of supercritical water were researched. The results show that the effect of the hydrogen bond on supercritical water is weakened obviously, and still exist. The bond length and the bond angle of the water molecular changed rapidly in the region of 648-748 K. The bond length and the bond angle of the water molecular changed slowly in 748-973 K. The characteristic peaks of radial distribution function increased with the increase of temperature in the region of 648-748 K, and decreased with the increase of temperature in the region of 748-973 K, which indicated that short range structure orderliness of water was changing with the increase of temperature. The self-diffusion coefficients of supercritical water were two orders of magnitude higher than ambient water, and increased with the increase of temperature, decreased with the increase of pressure.%采用分子动力学模拟方法,选用COMPASS力场,对超临界水的微观结构和扩散系数进行了研究.结果表明,在超临界区水分子的氢键作用明显减弱,但是仍有氢键存在.水分子的键长和键角在温度为648~748 K时变化迅速,在温度为748~973 K时变化很小.径向分布函数特征峰值在温度为648~748 K时随温度的升高而增大,在温度为748~973K时随温度升高而减小,表明水分子近程结构有序性随温度变化.超临界水自扩散系数是常温常压水的2个数量级,随温度升高而增大,随压力的升高而减小.

  5. Application of optimal prediction to molecular dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Barber, IV, John Letherman [Univ. of California, Berkeley, CA (United States)

    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.

  6. A molecular understanding of the dynamic mechanism of aquaporin osmosis

    CERN Document Server

    Shua, Liangsuo; Qian, Xin; Wanga, Xiyun; Lin, Yixin; Tan, Kai; Shu, Chaohui; Jin, Shiping

    2014-01-01

    AQPs (aquaporins), the rapid water channels of cells, play a key role in maintaining osmotic equilibrium of cells. In this paper, we reported the dynamic mechanism of AQP osmosis at the molecular level. A theoretical model based on molecular dynamics was carried out and verified by the published experimental data. The reflection coefficients ({\\sigma}) of neutral molecules are mainly decided by their relative size with AQPs, and increase with a third power up to a constant value 1. This model also indicated that the reflection coefficient of a complete impermeable solute can be smaller than 1. The H+ concentration of solution can influence the driving force of the AQPs by changing the equivalent diameters of vestibules surrounded by loops with abundant polar amino acids. In this way, pH of solution can regulate water permeability of AQPs. Therefore, an AQP may not only work as a switch to open or close, but as a rapid response molecular valve to control its water flow. The vestibules can prevent the channel b...

  7. Enhancing protein adsorption simulations by using accelerated molecular dynamics.

    Directory of Open Access Journals (Sweden)

    Christian Mücksch

    Full Text Available The atomistic modeling of protein adsorption on surfaces is hampered by the different time scales of the simulation ([Formula: see text][Formula: see text]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.

  8. Ab initio molecular dynamics using hybrid density functionals

    Science.gov (United States)

    Guidon, Manuel; Schiffmann, Florian; Hutter, Jürg; Vandevondele, Joost

    2008-06-01

    Ab initio molecular dynamics simulations with hybrid density functionals have so far found little application due to their computational cost. In this work, an implementation of the Hartree-Fock exchange is presented that is specifically targeted at ab initio molecular dynamics simulations of medium sized systems. We demonstrate that our implementation, which is available as part of the CP2K/Quickstep program, is robust and efficient. Several prescreening techniques lead to a linear scaling cost for integral evaluation and storage. Integral compression techniques allow for in-core calculations on systems containing several thousand basis functions. The massively parallel implementation respects integral symmetry and scales up to hundreds of CPUs using a dynamic load balancing scheme. A time-reversible multiple time step scheme, exploiting the difference in computational efficiency between hybrid and local functionals, brings further time savings. With extensive simulations of liquid water, we demonstrate the ability to perform, for several tens of picoseconds, ab initio molecular dynamics based on hybrid functionals of systems in the condensed phase containing a few thousand Gaussian basis functions.

  9. Molecular dynamics study on the structure I helium hydrate

    Institute of Scientific and Technical Information of China (English)

    CHENG Wei; WU Hucai; YE Xiaoqin; HOU Hongyu

    2004-01-01

    A 368- water molecule structure I gas hydrate, encased by the number of helium (He) molecules ranging from two to twenty-two, are calculated by molecular dynamical simulations. The potential TIP4P (transferable intermolecular potentical with four sites) is used for water interactions and Lennard-Jones for He-He and He-water interactions. He molecules do not affect the water lattice and can stabilize the hydrate when their concentration is small. A trough signature of He encased is found at 80~90 meV in the phonon density of states. He molecules prefer to be more off-center in 51262 cages. Heavier isotope He are energetically favorable to be filled in cages.

  10. Nano-tribology through molecular dynamics simulations

    Institute of Scientific and Technical Information of China (English)

    WANG; Hui(

    2001-01-01

    [1]Burkert, U., Allinger, N. L., Molecular Mechanics, York: Maple Press Company, 1982.[2]Daw, M. S. , Baskes, M. I., Embedded-atom method: derivation and application to impurities, surface and other defects in metals, Phys. Rev. B, 1984, 29: 6443-6453.[3]Frenke, D., Smit, B., Understanding Molecular Simulation, San Diego: Academic Press, 1996, 60-67, 125-140.[4]Granick, S., Motions and relaxation of confined liquids, Science, 1991, 253: 1374-1379.[5]Koplik, J., Banavar, J., Willemsen, J., Molecular dynamics of Poisewulle flow and moving contact line, Phys. Rev.Lett., 1988, 60: 1282-1285.[6]Hu, Y. Z., Wang, H., Guo, Y. et al., Simulation of lubricant rheology in thin film lubrication, Part I: simulation of Poiseuille flow, Wear, 1996, 196: 243-259.[7]Zou, K., Li, Z. J, Leng, Y. S. et al. , Surface force apparatus and its application in the study of solid contacts, Chinese Science Bulletin, 1999, 44: 268-271.[8]Stevens, M. , Mondello, M., Grest, G. et al. , Comparison of shear flow of hexadecane in a confined geometry and in bulk,J. Chem. Phys., 1997, 106: 7303-7314.[9]Huang, P., Luo, J. B., Wen, S. Z., Theoretical study on the lubrication failure for tthe lubricants with a limiting shear stress, Tribology International, 1999, 32: 421-426.[10]Ryckaert, J. P. , Bellemans. , A molecular dynamics of alkanes, Faraday Soc. , 1978, 66: 95-106.[11]Wang, H. , Hu, Y. Z., A molecular dynamics study on slip phenomenon at solid-liquid interface, in Proceedings of tthe First AICT, Beijing: Tsinghua University Press, 1998, 295-299.[12]Landman, U., Luedtke, W., Burnham, N. et al., Mechanisms and dynamics of adhesion, nanoindentation, and fracture, Science, 1990, 248: 454-461.[13]Leng, Y. S., Hu, Y. Z., Zheng, L. Q., Adhesive contact of flat-ended wedges: theory and computer experiments, Journal of Tribology, 1999, 121: 128-132.

  11. United polarizable multipole water model for molecular mechanics simulation

    Energy Technology Data Exchange (ETDEWEB)

    Qi, Rui; Wang, Qiantao; Ren, Pengyu, E-mail: pren@mail.utexas.edu [Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas 78712 (United States); Wang, Lee-Ping; Pande, Vijay S. [Department of Chemistry, Stanford University, Stanford, California 94305 (United States)

    2015-07-07

    We report the development of a united AMOEBA (uAMOEBA) polarizable water model, which is computationally 3–5 times more efficient than the three-site AMOEBA03 model in molecular dynamics simulations while providing comparable accuracy for gas-phase and liquid properties. In this coarse-grained polarizable water model, both electrostatic (permanent and induced) and van der Waals representations have been reduced to a single site located at the oxygen atom. The permanent charge distribution is described via the molecular dipole and quadrupole moments and the many-body polarization via an isotropic molecular polarizability, all located at the oxygen center. Similarly, a single van der Waals interaction site is used for each water molecule. Hydrogen atoms are retained only for the purpose of defining local frames for the molecular multipole moments and intramolecular vibrational modes. The parameters have been derived based on a combination of ab initio quantum mechanical and experimental data set containing gas-phase cluster structures and energies, and liquid thermodynamic properties. For validation, additional properties including dimer interaction energy, liquid structures, self-diffusion coefficient, and shear viscosity have been evaluated. The results demonstrate good transferability from the gas to the liquid phase over a wide range of temperatures, and from nonpolar to polar environments, due to the presence of molecular polarizability. The water coordination, hydrogen-bonding structure, and dynamic properties given by uAMOEBA are similar to those derived from the all-atom AMOEBA03 model and experiments. Thus, the current model is an accurate and efficient alternative for modeling water.

  12. Molecular modeling of the structure and dynamics of the interlayer and surface species of mixed-metal layered hydroxides: Chloride and water in hydrocalumite (Friedel's salt)

    Energy Technology Data Exchange (ETDEWEB)

    KALINICHEV,ANDREY G.; KIRKPATRICK,R. JAMES; CYGAN,RANDALL T

    2000-01-17

    The dynamical behavior of Cl{sup {minus}} and H{sub 2}O molecules in the interlayer and on the (001) surface of the Ca-aluminate hydrate hydrocalumite (Friedel's salt) over a range of temperatures from {minus}100 to 300 C is studied using the technique of isothermal-isobaric molecular dynamics computer simulations. This phase is currently the best available model compound for other, typically more disordered, mixed-metal layered hydroxides. The computed crystallographic parameters and density are in good agreement with available X-ray diffraction data and the force field developed for these simulations preserves the structure and density to within less than 2% of their measured values. In contrast to the highly ordered arrangement of the interlayer water molecules interpreted from the X-ray data, the simulations reveal significant dynamic disorder in water orientations. At all simulated temperatures, the interlayer water molecules undergo rapid librations (hindered hopping rotations) around an axis essentially perpendicular to the layers. This results in breaking and reformation of hydrogen bonds with the neighboring Cl{sup {minus}} anions and in a time-averaged nearly uniaxial symmetry at Cl{sup {minus}}, in good agreement with recent {sup 35}Cl NMR measurements. Power spectra of translational, vibrational, and vibrational motions of interlayer and surface Cl{sup {minus}} and H{sub 2}O were calculated as Fourier transforms of the atomic velocity autocorrelation functions and compared with the corresponding spectra and dynamics for a bulk aqueous solution. The ordered interlayer space has significant effects on the motions. Strong electrostatic attraction between interlayer water molecules and Ca atoms in the principal layer makes the Ca{hor_ellipsis}OH{sub 2} bond direction the preferred axis for interlayer water librations. The calculated diffusion coefficient of Cl{sup {minus}} as an outer-sphere surface complex is almost three times that of inner-sphere Cl

  13. Molecular mechanism for cavitation in water under tension

    CERN Document Server

    Menzl, Georg; Geiger, Philipp; Caupin, Frédéric; Abascal, Jose L F; Valeriani, Chantal; Dellago, Christoph

    2016-01-01

    Despite its relevance in biology and engineering, the molecular mechanism driving cavitation in water remains unknown. Using computer simulations, we investigate the structure and dynamics of vapor bubbles emerging from metastable water at negative pressures. We find that in the early stages of cavitation, bubbles are irregularly shaped and become more spherical as they grow. Nevertheless, the free energy of bubble formation can be perfectly reproduced in the framework of classical nucleation theory (CNT) if the curvature dependence of the surface tension is taken into account. Comparison of the observed bubble dynamics to the predictions of the macroscopic Rayleigh--Plesset (RP) equation, augmented with thermal fluctuations, demonstrates that the growth of nanoscale bubbles is governed by viscous forces. Combining the dynamical prefactor determined from the RP equation with the free energy of CNT yields an analytical expression for the cavitation rate that reproduces the simulation results very well over a w...

  14. Massively Parallel Reactive and Quantum Molecular Dynamics Simulations

    Science.gov (United States)

    Vashishta, Priya

    2015-03-01

    In this talk I will discuss two simulations: Cavitation bubbles readily occur in fluids subjected to rapid changes in pressure. We use billion-atom reactive molecular dynamics simulations on a 163,840-processor BlueGene/P supercomputer to investigate chemical and mechanical damages caused by shock-induced collapse of nanobubbles in water near silica surface. Collapse of an empty nanobubble generates high-speed nanojet, resulting in the formation of a pit on the surface. The gas-filled bubbles undergo partial collapse and consequently the damage on the silica surface is mitigated. Quantum molecular dynamics (QMD) simulations are performed on 786,432-processor Blue Gene/Q to study on-demand production of hydrogen gas from water using Al nanoclusters. QMD simulations reveal rapid hydrogen production from water by an Al nanocluster. We find a low activation-barrier mechanism, in which a pair of Lewis acid and base sites on the Aln surface preferentially catalyzes hydrogen production. I will also discuss on-demand production of hydrogen gas from water using and LiAl alloy particles. Research reported in this lecture was carried in collaboration with Rajiv Kalia, Aiichiro Nakano and Ken-ichi Nomura from the University of Southern California, and Fuyuki Shimojo and Kohei Shimamura from Kumamoto University, Japan.

  15. Ab initio centroid path integral molecular dynamics: Application to vibrational dynamics of diatomic molecular systems

    Science.gov (United States)

    Ohta, Yasuhito; Ohta, Koji; Kinugawa, Kenichi

    2004-01-01

    An ab initio centroid molecular dynamics (CMD) method is developed by combining the CMD method with the ab initio molecular orbital method. The ab initio CMD method is applied to vibrational dynamics of diatomic molecules, H2 and HF. For the H2