A continuum-atomistic method for incorporating Joule heating into classical molecular dynamics simulations

A hybrid atomistic-continuum method is presented for incorporating Joule heating into large-scale molecular dynamics (MD) simulations. When coupled to a continuum thermostat, the method allows resistive heating and heat transport in metals to be modeled without explicitly including electronic degrees of freedom. Atomic kinetic energies in a MD simulation are coupled via an ad hoc feedback loop to continuum current and heat transfer equations that are solved numerically on a finite difference grid (FDG). For resistive heating, the resistance in each region of the FDG is calculated from the experimental resistivity, atomic density, and average kinetic energy in the MD simulation. A network of resistors is established from which the potential at every FDG region is calculated given an applied voltage. The potential differences and the resistance between connected FDG regions are used to calculate the current between the two points and the heat generated from that current. This information is then added back into the atomic simulation. The method is demonstrated by simulating Joule heating and melting, along with associated changes in current, of single and bundles of metal nanowires, as well as a “pinched” wire under applied strain.     

Computer Simulation of Two-Dimensional Continuum Flows by the Direct Simulation Monte Carlo Method

Abstract

Computer simulations using particles are an attractive method to extract microscopic information of flow phenomena [1]. The molecular dynamics (MD) method, in which Newton's equations of motions are integrated, gives the temporal development of the system. In the MD simulation of fluid flows, the computational region is limited to atomistic scales [2]. On the other hand, the direct simulation Monte Carlo (DSMC) method, in which collisions of particles are made on a probabilistic basis, has a potential of treating a realistic system with a macroscopic scale length retaining the atomistic details. The DSMC method provides an efficient way to integrate the Boltzmann equation from the rarefied gas to the near-continuum region. Bird clarified the validity of the DSMC method in the near-continuum flow region [3]. However, the DSMC method has not been applied to the continuum region and compared with the continuum hydrodynamics.     

Examination of nanoflow in rectangular slits

This paper presents simulations of 3D nanoscale flow in rectangular channel with molecular dynamics simulation method. Rectangular cross section is a frequently encountered geometric shape for nanoscale flow problems. For a given cross sectional height h, we change the width w of the rectangular cross section and analyze the influence of w/h on the flow characteristics. The distributions of density, temperature, boundary slip and flow velocity inside the rectangular cross section are investigated in detail. Liquid argon material and Lennard-Jones potential are used in the simulations. The simulation results are also compared with Navier–Stokes solutions for rectangular channel flows.     

Structure, force, and energy of a double-stranded DNA oligonucleotide under tensile loads

The end-to-end stretching of a duplex DNA oligonucleotide has been studied using potential of mean force (PMF) calculations based on molecular dynamics (MD) simulations and atomic force microscopy (AFM) experiments. Near quantitative agreement between the calculations and experiments was obtained for both the extension length and forces associated with strand separation. The PMF calculations show that the oligonucleotide extends without a significant energetic barrier from a length shorter than A-DNA to a length 2.4 times the contour length of B-DNA at which the barrier to strand separation is encountered. Calculated forces associated with the barrier are 0.09±0.03 nN, based on assumptions concerning tip and thermal-activated barrier crossing contributions to the forces. Direct AFM measurements show the oligonucleotide strands separating at 2.6±0.8 contour lengths with a force of 0.13±0.05 nN. Analysis of the energies from the MD simulations during extension reveals compensation between increases in the DNA-self energy and decreases in the DNA-solvent interaction energy, allowing for the barrierless extension of DNA beyond the canonical B form. The barrier to strand separation occurs when unfavorable DNA interstrand repulsion cannot be compensated for by favorable DNA-solvent interactions. The present combination of single molecule theoretical and experimental approaches produces a comprehensive picture of the free energy surface of biological macromolecular structural transitions. Received: 2 June 1998 / Revised version: 25 January 1999 / Accepted: 11 February 1999     

Consistent Temperature Coupling with Thermal Fluctuations of Smooth Particle Hydrodynamics and Molecular Dynamics

We propose a thermodynamically consistent and energy-conserving temperature coupling scheme between the atomistic and the continuum domain. The coupling scheme links the two domains using the DPDE (Dissipative Particle Dynamics at constant Energy) thermostat and is designed to handle strong temperature gradients across the atomistic/continuum domain interface. The fundamentally different definitions of temperature in the continuum and atomistic domain – internal energy and heat capacity versus particle velocity – are accounted for in a straightforward and conceptually intuitive way by the DPDE thermostat. We verify the here-proposed scheme using a fluid, which is simultaneously represented as a continuum using Smooth Particle Hydrodynamics, and as an atomistically resolved liquid using Molecular Dynamics. In the case of equilibrium contact between both domains, we show that the correct microscopic equilibrium properties of the atomistic fluid are obtained. As an example of a strong non-equilibrium situation, we consider the propagation of a steady shock-wave from the continuum domain into the atomistic domain, and show that the coupling scheme conserves both energy and shock-wave dynamics. To demonstrate the applicability of our scheme to real systems, we consider shock loading of a phospholipid bilayer immersed in water in a multi-scale simulation, an interesting topic of biological relevance.     

Effect of surface roughness on slip flows in hydrophobic and hydrophilic microchannels by molecular dynamics simulation

The influences of surface roughness on the boundary conditions for a simple fluid flowing over hydrophobic and hydrophilic surfaces are investigated by molecular dynamics (MD) simulation. The degree of slip is found to decrease with surface roughness for both the hydrophobic and hydrophilic surfaces. The flow rates measured in hydrophobic channels are larger than those in hydrophilic channels with the presence of slip velocity at the walls. The simulation results of flow rate are correlated with the theoretical predictions according to the assumption of no slip boundary condition. The slip boundary condition also strongly depends on the shear rate near the surface. For hydrophobic surfaces, apparent fluid slips are observed on smooth and rough surfaces. For simple fluids flowing over a hydrophobic surface, the slip length increases linearly with shear rate for both the smooth and rough surfaces. Alternately, the slip length has a power law dependence on the shear rate for the cases of hydrophilic surfaces. It is observed that there is a no-slip boundary condition only when shear rate is low, and partial slip occurs when it exceeds a critical level.     

Molecular dynamics studies in nanoscale liquid structures: geometry and thermal effects on nanojet development

Conventional macroscopic jet theory relies heavily on experimental correlations which cannot be easily extended to the nanoscale regime. Moreover, the fluid dynamic effects at small length scales and their contribution to the development of nanoscale liquid structures are fundamentally different from their macroscopic counterparts. This coupled with the high spatial and temporal resolution requirements at nanoscale domains make molecular dynamics (MD) an excellent tool for studying such structures. In this study, the formation and breakup of nanojets (NJs) developing from high pressure into vacuum is investigated using MD based on non-Hamiltonian formulations. By ejecting the equilibrated argon atoms through various nozzle geometries and diameters, nanoscale jet flows were generated. The dependence of the jet structure on nozzle geometry and diameter is studied. The influence of geometry on NJ formation is also studied along with issues involved in the equilibration and thermostat coupling parameter. Various thermostats are compared to understand the role they play in MD simulations of liquid nanostructures. Tuning of the thermostat coupling parameter has also been discussed. The jet breakup phenomenon is analysed and a comparative study, vis-à-vis, well-established continuum and stochastic models, is attempted.     

The nanoindentation responses of nickel surfaces with different crystal orientations

Molecular dynamics (MD) simulations are applied to elucidate the anisotropic characteristics in the material responses for crystallographic nickel substrates with (100), (110) and (111) surface orientations during nanoindentation, compensating for the experimental limitation of nanoindentation—particularly for pure nickel substrates of three crystallographic orientations. This study examines several factors under indentation: three-dimensional phases of plastic deformation which correspond to atomic stress distributions, pile-up patterns at maximum indentation depth, and extracted material properties at different crystallographic orientations. The present results reveal that the strain energy of the substrate exerted by the tip is stored by the formation of the homogeneous nucleation, and is dissipated by the dislocation sliding of the {111} plane. The steep variations of the indentation curve from the local peak to the local minimums are affected by the numbers of slip angle of {111} sliding plane. The pile-up patterns of the three nickel substrates prove that the crystalline nickel materials demonstrate the pile-up phenomenon from nanoindentation on the nano-scale. The three crystallographic nickel substrates exhibit differing amounts of pile-up dislocation spreading at different crystallographic orientations. Finally, the effects of surface orientation in material properties of FCC nickel material on the nano-scale are observable through the slip angle numbers of {111} sliding planes which influence hardness values, as well as the cohesive energy of different crystallographic surfaces that indicate Young's modulus.     

Viscous Friction between Crystalline and Amorphous Phase of Dragline Silk

The hierarchical structure of spider dragline silk is composed of two major constituents, the amorphous phase and crystalline units, and its mechanical response has been attributed to these prime constituents. Silk mechanics, however, might also be influenced by the resistance against sliding of these two phases relative to each other under load. We here used atomistic molecular dynamics (MD) simulations to obtain friction forces for the relative sliding of the amorphous phase and crystalline units of Araneus diadematus spider silk. We computed the coefficient of viscosity of this interface to be in the order of 10² Ns/m² by extrapolating our simulation data to the viscous limit. Interestingly, this value is two orders of magnitude smaller than the coefficient of viscosity within the amorphous phase. This suggests that sliding along a planar and homogeneous surface of straight polyalanine chains is much less hindered than within entangled disordered chains. Finally, in a simple finite element model, which is based on parameters determined from MD simulations including the newly deduced coefficient of viscosity, we assessed the frictional behavior between these two components for the experimental range of relative pulling velocities. We found that a perfectly relative horizontal motion has no significant resistance against sliding, however, slightly inclined loading causes measurable resistance. Our analysis paves the way towards a finite element model of silk fibers in which crystalline units can slide, move and rearrange themselves in the fiber during loading.     

The nicotinic acetylcholine receptor: from molecular model to single-channel conductance

The nicotinic acetylcholine receptor (nAChR) is the archetypal ligand-gated ion channel. A model of the α7 homopentameric nAChR is described in which the pore-lining M2 helix bundle is treated atomistically and the remainder of the molecule is treated as a “low resolution” cylinder. The surface charge on the cylinder is derived from the distribution of charged amino acids in the amino acid sequence (excluding the M2 segments). This model is explored in terms of its predicted single-channel properties. Based on electrostatic potential profiles derived from the model, the one-dimensional Poisson-Nernst-Planck equation is used to calculate single-channel current/voltage curves. The predicted single-channel conductance is three times higher (ca. 150 pS) than that measured experimentally, and the predicted ion selectivity agrees with the observed cation selectivity of nAChR. Molecular dynamics (MD) simulations are used to estimate the self-diffusion coefficients (D) of water molecules within the channel. In the narrowest region of the pore, D is reduced ca. threefold relative to that of bulk water. Assuming that the diffusion of ions scales with that of water, this yields a revised prediction of the single-channel conductance (ca. 50 pS) in good agreement with the experimental value. We conclude that combining atomistic (MD) and continuum electrostatics calculations is a promising approach to bridging the gap between structure and physiology of ion channels. Received: 2 August 1999 / Revised version: 5 November 1999 / Accepted: 9 November 1999     

Leap-dynamics: efficient sampling of conformational space of proteins and peptides in solution

A molecular simulation scheme, called Leap-dynamics, that provides efficient sampling of protein conformational space in solution is presented. The scheme is a combined approach using a fast sampling method, imposing conformational 'leaps' to force the system over energy barriers, and molecular dynamics (MD) for refinement. The presence of solvent is approximated by a potential of mean force depending on the solvent accessible surface area. The method has been successfully applied to N-acetyl-L-alanine-N-methylamide (alanine dipeptide), sampling experimentally observed conformations inaccessible to MD alone under the chosen conditions. The method predicts correctly the increased partial flexibility of the mutant Y35G compared to native bovine pancreatic trypsin inhibitor. In particular, the improvement over MD consists of the detection of conformational flexibility that corresponds closely to slow motions identified by nuclear magnetic resonance techniques.     

Thermoregulation during swimming and diving in bottlenose dolphins, Tursiops truncatus

Heat transfer from the periphery is an important thermoregulatory response in exercising mammals. However, when marine mammals submerge, peripheral vasoconstriction associated with the dive response may preclude heat dissipation at depth. To determine the effects of exercise and diving on thermoregulation in cetaceans, we measured heat flow and skin temperatures of bottlenose dolphins (Tursiops truncatus) trained to follow a boat and to dive to 15 m. The results demonstrated that skin temperatures usually remained within 1 °C of the water after all exercise levels. Heat flow from peripheral sites (dorsal fin and flukes) increased over resting values immediately after exercise at the water surface and remained elevated for up to 20 min. However, post-exercise values for heat flow from the flukes and dorsal fin decreased by 30–67% when dolphins stationed at 15 m below the surface. The pattern in heat flow was reversed during ascent. For example, mean heat flow from the flukes measured at 5 m depth, 40.10 ± 2.47 W · m⁻², increased by 103.2% upon ascent. There is some flexibility in the balance between thermal and diving responses of dolphins. During high heat loads, heat transfer may momentarily increase during submergence. However, the majority of excess heat in dolphins appears to be dissipated upon resurfacing, thereby preserving the oxygen-conserving benefits of the dive response. Accepted: 4 January 1999     

Reverse flow in roots of Sesbania rostrata measured using the constant power heat balance method

This investigation was performed to examine qualitatively and quantitatively the reverse flow in partially dried roots of Sesbania rostrata using the constant power heat balance method. First, a semi-empirical technique for estimating sheath conductance of sap-flow sensors without assuming that sap flow is zero at night was proposed. Sap flow measured with the heat balance method was compared with water uptake as measured by a potometric method. Sap flow was overestimated by 56·1% for a 3·3-mm-diameter root, and by 40·0% for 6·1 mm and 33·3% for 8·8 mm roots. However, high correlation coefficients between the rates of water uptake and sap flow demonstrated that calibration would provide reliable values for root sap flow. To detect reverse flow, a split root experiment was conducted using a S. rostrata plant with its root system divided between dry and wet compartments. Daily sap flow of the drying compartment declined whereas that in ‘wet’ root increased, suggesting that the decrease in water uptake by ‘dry’ roots was offset by the ‘wet’ roots. Reverse flow was observed at night in the root on the dry side of the container when the soil water potential was less than –0·30 MPa. The total amount of water released into the soil during the night period was estimated to be 22·5 g.     

Bionic Design and Finite Element Analysis of Elbow in Ice Transportation Cooling System

With the increase in mining depth, mine heat harm has appeared to be more prominent. The mine heat harm could be resolvedor reduced by ice refrigeration. Thus, ice transportation through pipeline becomes a critical problem; typically flowresistance occurs in the elbow. In the present study, according to the analysis of the surface morphology of fish scale, abiomimetic functional surface structure for the interior wall of elbow is designed. Based on the theory of liquid-solid two phaseflow, a CFD numerical simulation of ice-water mixture flowing through the elbow is carried out using finite element method.Conventional experiments of pressure drop and flow resistance for both bionic and common elbows are conducted to test theeffect of the bionic elbow on flow resistance reduction. It is found that with the increase in the ice mass fraction in the ice-watermixture, the effect of bionic elbow on resistance reduction becomes more obvious.     

Boundary layer properties of highly dissected leaves: an investigation using an electrochemical fluid tunnel

Abstract. A method for modelling heat and mass transfer by diffusion-controlled electrode reactions in a fluid tunnel is described. In this procedure, a nickelplated leaf functions as a test electrode, and the convective transfer of ions to the leaf cathode in an electrolyte-filled flow tunnel is measured as a function of flow rate. The method permits the simulation of water vapour and heat transfer, and in particular, the determination of boundary layer conductances, by analogy with observed ion transfer. The approach is applicable to many problems in modelling heat and mass transfer between leaves and their surroundings, and is especially useful in examining the properties of leaves in which surface characteristics or overall shape are complex. Using this method, the properties of the highly dissected leaves of Achillea lanulosa with regard to forced convection were investigated. The leaves showed high transfer conductances, indicating that the effective unit of heat transfer was probably the individual leaf subelements. Conductances tended to be greater and effective characteristic dimensions smaller for the larger, more open leaves of a lower altitude population in contrast with leaves from high altitude plants. While the results provide insight into the properties of these complex leaf shapes, difficulties in interpreting the findings are discussed, and a number of exploratory approaches are suggested for data analysis and interpretation.     

Peptides and Peptoids - A Systematic Structure Comparison

A systematic analysis of the conformational space of the basic structure unit of peptoids in comparison to the corresponding peptide unit was performed based on ab initio MO theory and complemented by molecular mechanics (MM) and molecular dynamics (MD) calculations both in the gas phase and in aqueous solution.The calculations show three minimum conformations denoted as C_7ß, a_D and a that do not correspond to conformers on the gas phase peptide potential energy hypersurface. The influence of aqueous solvation was estimated by means of continuum models. The MD simulations indicate the a_D form as the preferred conformation in solution both in cis and trans peptide bond orientations.     

Molecular dynamics simulation: A new way to understand the functionality of the endothelial glycocalyx

Endothelial glycocalyx (EG) is a carbohydrate-rich layer which lines the lumen side of blood vessel walls. The EG layer is directly exposed to blood flow. The unique physiological location and its strongly coupled interaction with blood flow allow the EG layer to modulate microvascular mass transport and to sense and transmit mechanical signals from the passing blood. Molecular dynamics (MD) simulation is a computational method which focuses on atomic/molecular behavior at the microscale. The last two decades have witnessed a substantial increase in number and a broadening in scope regarding applications of MD in a wide spectrum of areas, including EG-related research. In this mini-review, MD works which solve EG-related problems and provide new insights into the functionality of EG are considered. Challenges of the MD method in EG research are articulated, and the future of MD in solving EG-related problems is also evaluated.     

Importance of explicit salt ions for protein stability in molecular dynamics simulation.

The accurate and efficient treatment of electrostatic interactions is one of the challenging problems of molecular dynamics simulation. Truncation procedures such as switching or shifting energies or forces lead to artifacts and significantly reduced accuracy. The particle mesh Ewald (PME) method is one approach to overcome these problems by providing a computationally efficient means of calculating all long-range electrostatic interactions in a periodic simulation box by use of fast Fourier transformation techniques. For the application of the PME method to the simulation of a protein with a net charge in aqueous solution, counterions are added to neutralize the system. The usual procedure is to add charge-balancing counterions close to charged residues to neutralize the protein surface. In the present article, we show that for MD simulation of a small protein of marginal stability, the YAP-WW domain, explicit modeling of 0.2 M ionic strength (in addition to the charge-balancing counterions) is necessary to maintain a stable protein structure. Without explicit ions throughout the periodic simulation box, the charge-balancing counterions on the protein surface diffuse away from the protein, resulting in destruction of the beta-sheet secondary structure of the WW domain.     

Molecular dynamics simulation of helium–argon gas mixture under various wall conditions

As computational capabilities increase, molecular dynamics (MD) simulations become important tools of simulating reality. These simulations are especially useful for compressible gas mixture problems. In this study, binary diffusion of helium and argon was examined using a hard-sphere MD simulation method. For the sake of computational speed, low spacing ratios were chosen. Binary mass diffusion of gases in two equally sized halves of a box was simulated for identical initial kinetic energies and number densities. It has been noted that a purely mass diffusion mechanism of different gases is not physically possible. The resultant gas mixtures of several diffusion simulations were used as initial conditions for combined heat transfer – Couette flow, and heating and cooling experiments. The results showed the interesting behaviour of the mixture, which was subjected to various wall conditions. Energy of heavier molecules is found to be more sensitive to the wall velocities and less sensitive to the wall temperatures than lighter molecules. Diffusion, heat transfer, viscosity and heat capacity coefficients are deduced as well.