Molecular dynamics simulation on influence of temperature effect on electro-coalescence behavior of nano-droplets

In electric dehydration of crude oil, the dewatering efficiency can be improved by raising emulsion temperature properly which reduces the viscosity of crude oil. However, it should be noticed that the emulsion temperature does not only affect the emulsion viscosity but also nano-droplets dynamics behavior which impacts the coalescence efficiency either. Therefore the influence of temperature effect on the electro-coalescence of nano-droplets is studied by a molecular dynamics method. The results show that the temperature presents an active or negative effect, depending on the competitive relation between electrostatic interaction and thermal motion. Two stages are distinguished according to the dominant mechanism. During stage I, governed by the electrostatic interaction, lower temperature promotes the polarization and leads to an acceleration of the droplets coalescence, but higher temperature restrains the coalescence process due to molecules thermal motion breaking the polarization process. During stage II, governed by the thermal motion, lower temperature improves the coalescence because of a diffusion effect, but higher temperature deteriorates electro-coalescence because of a violent molecular thermal motion. Additionally, hydrogen bond and radial distribution functions are obtained by statistics to describe droplets micromorphology, which explains the reason why the droplet forms longer chain structure at the critical electric field.     

Monte-Carlo simulation of free-radical decay as a probe of local and collective dynamics in polymer molecules

The effect of molecular mobility on the stability of free radicals in amorphous polymers was investigated by a Monte-Carlo (MC) method. Crank, crankshaft-like, kink and double kink were used as the various types of movements of submolecular structures. This work introduces the librational motions of these structures and formulates the methodology for their incorporation into the MC method. The results show that the presence of librational motion significantly influences both transfer and the decay of free radicals.     

Molecular dynamics simulation of a pressure-driven liquid transport process in a cylindrical nanopore using two self-adjusting plates

Fluid transport through a nanopore in a membrane was investigated by using a novel molecular dynamics approach proposed in this study. The advantages of this method, relative to dual-control-volume grand-canonical molecular dynamics method, are that it eliminates disruptions to the system dynamics that are normally created by inserting or deleting particles from control volumes, and that it functions well for dense systems due to the number of particles being fixed in the system. Using the proposed method, we examined liquid argon transport through a nanopore by performing nonequilibrium molecular dynamics (NEMD) simulations under different back pressures. Validation of the code was performed by comparing simulation results to published experimental data obtained under equilibrium conditions. NEMD results show that constant pressure difference across the membrane was readily achieved.     

On the influence of charged side chains on the folding-unfolding equilibrium of beta-peptides: a molecular dynamics simulation study

The influence of charged side chains on the folding-unfolding equilibrium of beta-peptides was investigated by means of molecular dynamics simulations. Four different peptides containing only negatively charged side chains, positively charged side chains, both types of charged side chains (with the ability to form stabilizing salt bridges) or no charged side chains were studied under various conditions (different simulation temperatures, starting structures and solvent environment). The NMR solution structure in methanol of one of the peptides (A) has already been published; the synthesis and NMR analysis of another peptide (B) is described here. The other peptides (C and D) studied herein have hitherto not been synthesized. All four peptides A-D are expected to adopt a left-handed 3(14)-helix in solution as well as in the simulations. The resulting ensembles of structures were analyzed in terms of conformational space sampled by the peptides, folding behavior, structural properties such as hydrogen bonding, side chain-side chain and side chain-backbone interactions and in terms of the level of agreement with the NMR data available for two of the peptides. It was found that the presence of charged side chains significantly slows down the folding process in methanol solution due to the stabilization of intermediate conformers with side chain-backbone interactions. In water, where the solvent competes with the solute-solute polar interactions, the folding process to the 3(14)-helix is faster in the simulations.     

Spatial regimes in the dynamics of polyolefins: collective motion

Molecular simulation is used to characterize the spatial dependence of collective motion in four saturated hydrocarbon polymers. The observable is the distinct intermediate scattering function, as measured in coherent quasielastic neutron scattering experiments. Ranges of 0.01-1000 ps in time and 2-14 A in spatial scale are covered. In this time range, a two-step relaxation, consisting of a fast exponential decay and a slower stretched decay, is observed for all spatial scales. The relaxation times for the fast process are very similar to those obtained by following self motion, with a small modulation of relaxation times near the peak in the static structure factor which is well described by the narrowing picture suggested by de Gennes. For the slow process, self and collective relaxation times have larger numerical differences and follow different scaling with spatial scale. The modulation of slow relaxation times is larger than that observed for the fast process, but is overestimated by the de Gennes prediction, which only works qualitatively.     

Inhomogeneity effects on the structure and dynamics of water at the surface of a membrane: a computer simulation study

The authors report the structural and dynamical properties of water interacting with the surface of a lipid bilayer. Three regions have been identified, which show different dynamical regimes of water: a region of strong water-solute interaction, a transition region, and the bulk water region. The dynamics of the strong-interacting water is dominated by caging effects, as shown by the analysis of the self-intermediate scattering function, and by the disrupture of water's hydrogen bond network, while the smooth transition to bulk water is traced back to the roughness of the bilayer surface.     

The effect of pressure on the hydration structure around hydrophobic solute: a molecular dynamics simulation study

Molecular dynamics simulations are performed to study the effects of pressure on the hydrophobic interactions between neopentane molecules immersed in water. Simulations are carried out for five different pressure values ranging from 1 atm to 8000 atm. From potential of mean force calculations, we find that with enhancement of pressure, there is decrease in the well depth of contact minimum (CM) and the relative stability of solvent separated minimum over CM increases. Lower clustering of neopentane at high pressure is also observed in association constant and cluster-structure analysis. Selected site-site radial distribution functions suggest efficient packing of water molecules around neopentane molecules at elevated pressure. The orientational profile calculations of water molecules show that the orientation of water molecules in the vicinity of solute molecule is anisotropic and this distribution becomes flatter as we move away from the solute. Increasing pressure slightly changes the water distribution. Our hydrogen bond properties and dynamics calculations reveal pressure-induced formation of more and more number of water molecules with five and four hydrogen bond at the expense of breaking of two and three hydrogen bonded water molecules. We also find lowering of water-water continuous hydrogen bond lifetime on application of pressure. Implication of these results for relative dispersion of hydrophobic molecules at high pressure are discussed.     

Packing effects on argon and methanol adsorption inside graphitic cylindrical and slit pores: a GCMC simulation study

Using Grand Canonical Monte Carlo simulation, we have studied the effects of confinement on argon and methanol adsorption in graphitic cylindrical and slit pores. Linear chain, zigzag and incomplete helical packing are observed for argon adsorption in cylindrical pores. However, for methanol adsorption different features appear because the electrostatic interactions favour configurations that maximize the hydrogen bonding among methanol molecules. We have found zigzag chains with hydrogen-bonded structures for methanol adsorption in cylindrical and slit pores. To investigate how dense the adsorbed phase is and how many molecules could be packed per unit physical volume of the solid, we consider two different definitions of pore density; one based on the physical volume and the other on the accessible volume. That based on accessible volume gives a measure of the fluid density, while that based on the physical volume gives a measure of how much adsorbate can be stored per unit volume of the adsorbent. It is found that the adsorbate is denser in cylindrical pores, but that slit pores can pack more molecules per unit solid volume. We also discuss the effects on the isosteric heat of argon and methanol of pore size, pore geometry and loading.     

Boundary effect on electrophoresis: finite cylinder in a cylindrical pore

The boundary effect on electrophoresis is investigated by considering a finite cylindrical particle moving along the axis of a long cylindrical pore under conditions of low surface potential and weak applied electric field. The influence of the thickness of the double layer, the aspect ratio of a particle, the ratio particle radius/pore radius, and the charged conditions of the surfaces of the particle and pore on the electrophoretic behavior of a particle are investigated. We show that the effect of the aspect ratio of a particle on its electrophoretic behavior for the case where the particle is charged and the pore is uncharged is larger than that for the case where the particle is uncharged and the pore is charged. Also, depending on the parameters chosen, increasing the aspect ratio of a particle can either promote or hinder its movement, which is not reported in previous studies, and can play a role in electrophoresis measurements. Because both the electric and the flow fields in the gap between the particle and the pore are mediated by those near the top and the end of the particle, the end effect is large when the double layer is thick.     

Dynamics of benzene guest inside a self-assembled cylindrical capsule: a combined solid-state 2H NMR and molecular dynamics simulation study

The reorientational dynamics of benzene-d(6) molecules hosted into the cavity of a cavitand-based, self-assembled capsule was investigated by Molecular Dynamics (MD) simulations and temperature-dependent solid-state (2)H NMR spectroscopy. MD simulations were preliminarily performed to assess the motional models of the guest molecules inside the capsules. An in-plane fast reorientation of the benzene guest around the C(6) symmetry axis (B1 motion), characterized by correlation times of the order of picoseconds, was predicted with an activation barrier ( approximately 8 kJ/mol) very similar to that found for neat benzene in the liquid state. An out-of-plane reorientation corresponding to a nutation of the C(6) symmetry axis in a cone angle of 39 degrees (B2 motion, 373 K) with an activation barrier ( approximately 39 kJ/mol) definitely larger than that of liquid benzene was also anticipated. In the temperature range 293-373 K correlation times of the order of a nanosecond have been calculated and a transition from fast to slow regime in the (2)H NMR scale has been predicted between 293 and 173 K. (2)H NMR spectroscopic analysis, carried out in the temperature range 173-373 K on the solid capsules containing the perdeuterated guest (two benzene molecules/capsule), confirmed the occurrence of the B1 and B2 motions found in slow exchange in the (2)H NMR time scale. Line shape simulation of the (2)H NMR spectral lines permitted defining a cone angle value of 39 degrees at 373 K and 35 degrees at 173 K for the nutation axis. The T(1) values measured for the (2)H nuclei of the encapsulated aromatic guest gave correlation times and energetic barrier for the in-plane motion B1 in fine agreement with theoretical calculation. The experimental correlation time for B2 as well as the corresponding energetic barrier are in the same range found for B1. A molecular mechanism for the encapsulated guest accounting for the B1 and B2 motions was also provided.     

Communication: effects of stress on the tube confinement potential and dynamics of topologically entangled rod fluids

A microscopic theory for the effect of applied stress on the transverse topological confinement potential and slow dynamics of heavily entangled rigid rods is presented. The confining entanglement force localizing a polymer in a tube is predicted to have a finite strength. As a consequence, three regimes of terminal relaxation behavior are predicted with increasing stress: accelerated reptation due to tube widening (dilation), relaxation via deformation-assisted activated transverse barrier hopping, and complete destruction of the lateral tube constraints corresponding to microscopic yielding or a disentanglement transition.     

The effect of solvent dynamics on the low frequency collective motions of DNA in solution and unoriented films

Infrared spectroscopy is used to probe the dynamics of in vitro samples of DNA prepared as solutions and as solid unoriented films. The lowest frequency DNA mode identified in the far-infrared spectra of the DNA samples is found to shift in frequency when the solvent influence in the hydration shell is altered. The lowest frequency mode also has characteristics that are similar to beta-relaxations identified in other glass forming polymers.     

Molecular dynamics simulation study on the inhibitory effects of choline-O-sulfate on hIAPP protofibrilation

Type 2 diabetes mellitus (T2Dm) is a neurodegenerative disease, which occurs due to the self-association of human islet amyloid polypeptide (hIAPP), also known as human amylin. It was reported experimentally that choline-O-sulfate (COS), a small organic molecule having a tertiary amino group and sulfate group, can prevent the aggregation of human amylin without providing the mechanism of the action of COS in the inhibition process. In this work, we investigate the influence of COS on the full-length hIAPP peptide by performing 500 ns classical molecular dynamics simulations. From pure water simulation (without COS), we have identified the residues 11–20 and 23–36 that mainly participate in the fibril formation, but in the presence of 1.07 M COS these residues become totally free of β-sheet conformation. Our results also show that the sulfate oxygen of COS directly interacts with the peptide backbone, which leads to the local disruption of peptide–peptide interaction. Moreover, the presence of favorable peptide-COS vdW interaction energy and high coordination number of COS molecules in the first solvation shell of the peptide indicates the hydrophobic solvation of the peptide residues by COS molecules, which also play a crucial role in the prevention of β-sheet formation. Finally, from the potential of mean force (PMFs) calculations, we observe that the free energy between two peptides is more negative in the absence of COS and with increasing concentration of COS, it becomes unfavorable significantly indicating that the peptide dimer formation is most stable in pure water, which becomes less favorable in the presence of COS. © 2019 Wiley Periodicals, Inc.     

Chloride concentration and temperature effects on the hydration of Th(IV) ion: a molecular dynamics simulation

Molecular dynamics simulations have been performed to investigate the structural and dynamical properties of the second hydration shell of Th⁴⁺ ion at various chloride concentrations and temperatures. When the concentration increases (ca. 5 M), the hydration of Th⁴⁺ ion involves the displacement of the water molecules by Cl⁻ ligand and slightly decreases the total coordination number. The residence time of water molecules in the second hydration shell decreases as a function of increasing solution temperature.     

Drag on two nonuniformly structured flocs moving along the axis of a cylindrical tube

The boundary effect on the drag on two identical, nonuniformly structured flocs moving along the axis of a cylindrical tube filled with a Newtonian fluid is investigated at a small to medium larger Reynolds number. A two-layer model is adopted to simulate various possible structures of a floc, and the flow field inside is described by Darcy–Brinkman model. The results of numerical simulation reveal that a convective flow is present in the rear region of a floc when Reynolds number is on the order of 40. The presence of the tube wall and/or the porous structure of a floc has the effect of reducing that convective flow. For a fixed level of the volume-average permeability of a floc, the influence of the tube wall on the drag depends upon floc structure; the influence on a nonuniformly structured floc is more significant than that on a uniformly structured floc. The more nonuniform the floc structure, the more appreciable the deviation of the drag coefficient–Reynolds number curve from a Stokes’-law-like relation becomes. The smaller the volume-average permeability of a floc and/or the smaller the separation distance between the two flocs, the greater is the deviation, but the presence of the tube wall has the effect of reducing that deviation.     

Differential effects of cholesterol, ergosterol and lanosterol on a dipalmitoyl phosphatidylcholine membrane: a molecular dynamics simulation study

Lipid raft/domain formation may arise as a result of the effects of specific sterols on the physical properties of membranes. Here, using molecular dynamics simulation, we examine the effects of three closely-related sterols, ergosterol, cholesterol, and lanosterol, at a biologically relevant concentration (40 mol %) on the structural properties of a model dipalmitoyl phosphatidylcholine (DPPC) membrane at 309 and 323 K. All three sterols are found to order the DPPC acyl tails and condense the membrane relative to the DPPC liquid-phase membrane, but each one does this to a significantly different degree. The smooth alpha-face of ergosterol, together with the presence of tail unsaturation in this sterol, leads to closer interaction of ergosterol with the lipids and closer packing of the lipids with each other, so ergosterol has a higher condensing effect on the membrane, as reflected by the area per lipid. Moreover, ergosterol induces a higher proportion of trans lipid conformers, a thicker membrane, and higher lipid order parameters and is aligned more closely with the membrane normal. Ergosterol also positions itself closer to the bilayer/water interface. In contrast, the rough alpha-face of lanosterol leads to a less close interaction of the steroid ring system with the phospholipid acyl chains, and so lanosterol orders, straightens, and packs the lipid acyl chains less well and is less closely aligned with the membrane normal. Furthermore, lanosterol lies closer to the relatively disordered membrane center than do the other sterols. The behavior of cholesterol in all the above respects is intermediate between that of lanosterol and ergosterol. The findings here may explain why ergosterol is the most efficient of the three sterols at promoting the liquid-ordered phase and lipid domain formation and may also furnish part of the explanation as to why cholesterol is evolutionarily preferred over lanosterol in higher-vertebrate plasma membranes.     

Anisotropy on the collective dynamics of water confined in swelling clay minerals

Collective excitations of water confined in the interlayer space of swelling clay minerals were studied by means of inelastic neutron scattering. The effect of bidimensional confinement on the dynamics of the interlayer water was investigated by using a synthetic Na-saponite sample with a general formula of Si(7.3)Al(0.7)Mg(6)O(20)(OH)(4)Na(0.7) in a bilayer hydration state. Experimental results reveal two inelastic signals, different from those described for bulk water with a clear anisotropy on the low-energy excitation of the collective dynamics of interlayer water, this difference being stronger in the perpendicular direction. Results obtained for the parallel direction follow the same trend as bulk water, and the effect of the confinement is mainly manifested from the fact that clay interlayer water is more structured than bulk water. Data obtained in the perpendicular direction display a nondispersive behavior below a cutoff wavenumber value, Q(c), indicating a nonpropagative excitation below that value. Molecular dynamics simulations results agree qualitatively with the experimental results.     

The mixed alkali effect in ionically conducting glasses revisited: a study by molecular dynamics simulation

When more than two kinds of mobile ions are mixed in ionic conducting glasses and crystals, there is a non-linear decrease of the transport coefficients of either type of ion. This phenomenon is known as the mixed mobile ion effect or Mixed Alkali Effect (MAE), and remains an unsolved problem. We use molecular dynamics simulation to study the complex ion dynamics in ionically conducting glasses including the MAE. In the mixed alkali lithium-potassium silicate glasses and related systems, a distinct part of the van Hove functions reveals that jumps from one kind of site to another are suppressed. Although, consensus for the existence of preferential jump paths for each kind of mobile ions seems to have been reached amongst researchers, the role of network formers and the number of unoccupied ion sites remain controversial in explaining the MAE. In principle, these factors when incorporated into a theory can generate the MAE, but in reality they are not essential for a viable explanation of the ion dynamics and the MAE. Instead, dynamical heterogeneity and "cooperativity blockage" originating from ion-ion interaction and correlation are fundamental for the observed ion dynamics and the MAE. Suppression of long range motion with increased back-correlated motions is shown to be a cause of the large decrease of the diffusivity especially in dilute foreign alkali regions. Support for our conclusion also comes from the fact that these features of ion dynamics are common to other ionic conductors, which have no glassy networks, and yet they all exhibit the MAE.     

Molecular dynamics simulation of the dielectric constant of water: the effect of bond flexibility

The role of bond flexibility on the dielectric constant of water is investigated via molecular dynamics simulations using a flexible intermolecular potential SPC/Fw [Y. Wu, H. L. Tepper, and G. A. Voth, J. Chem. Phys. 128, 024503 (2006)]. Dielectric constants and densities are reported for the liquid phase at temperatures of 298.15 K and 473.15 K and the supercritical phase at 673.15 K for pressures between 0.1 MPa and 200 MPa. Comparison with both experimental data and other rigid bond intermolecular potentials indicates that introducing bond flexibility significantly improves the prediction of both dielectric constants and pressure-temperature-density behavior. In some cases, the predicted densities and dielectric constants almost exactly coincide with experimental data. The results are analyzed in terms of dipole moments, quadrupole moments, and equilibrium bond angles and lengths. It appears that bond flexibility allows the molecular dipole and quadrupole moment to change with the thermodynamic state point, and thereby mimic the change of the intermolecular interactions in response to the local environment.     

The effect of hydrogen bonding on oligoleucine structure in water: A molecular dynamics simulation study

Molecular dynamics simulations were conducted in order to improve our understanding of the forces that determine polyleucine chains conformations and govern polyleucine self-assembly in aqueous solutions. Simulations of 10 repeat unit oligoleucine in aqueous solution were performed using the optimized potential for liquid simulations (OPLS) - all atom force field using the canonical ensemble for a minimum of 1.3 ns. These simulations provided information on conformations, chain collapse and intermolecular aggregation. Simulations indicate that single isotactic oligoleucine chains in dilute solution assume tightly packed, regular hairpin conformations while atactic oligoleucine assumes a much less regular and less compact structure. The regular, compact collapsed isotactic chain exhibited a greater degree of intramolecular hydrogen bonding and an increased level of hydrophobic t-butyl functional group aggregation compared to the atactic chain. This occurs at the expense of reduced leucine-water hydrogen bonding.