Slip boundaries in nanopores

The flow of liquid water confined within slit pores formed from amorphous surfaces of carbon and polydimethylsiloxane (PDMS) has been investigated using molecular dynamics techniques. For PDMS (including plasma treated forms) the slip length is found to be very small, and there are essentially stick boundary conditions. The slip lengths for amorphous carbon surfaces are significant; however, they are much smaller than those measured experimentally for nanopipes. We show, for the first time, that the slip length can be predicted using the Sokhan–Quirke equation for amorphous surfaces using only equilibrium properties.     

Cation transport in nanopores

Using periodic boundary conditions and external electric potential field, we have simulated an ion current flow through a flexible nanopore using cations and an explicit extended simple point charge (SPC/E) water with molecular dynamics simulation. The simulation voltages range goes beyond the usual ionic channel measurements ( ± 1 V) and yields useful information about density profiles, current density distribution and current–voltage (I–V) characteristics.     

Transport diffusivities of fluids in nanopores by non-equilibrium molecular dynamics simulation

We present a method to study fluid transport through nanoporous materials using highly efficient non-equilibrium molecular dynamics simulations. A steady flow is induced by applying an external field to the fluid particles within a small slab of the simulation cell. The external field generates a density gradient between both sides of the porous material, which in turn triggers a convective flux through the porous medium. The heat dissipated by the fluid flow is released by a Gaussian thermostat applied to the wall particles. This method is effective for studying diffusivities in a slit pore as well as more natural, complex wall geometries. The dependence of the diffusive flux on the external field sheds light on the transport diffusivities and allows a direct calculation of effective diffusivities. Both pore and fluid particle interactions are represented by coarse-grained molecular models in order to present a proof-of-concept and to retain computational efficiency in the simulations. The application of the method is demonstrated in two different scenarios, namely the effective mass transport through a slit pore and the calculation of the effective self-diffusion through this system. The method allows for a distinction between diffusive and convective contributions of the mass transport.     

Shear rate dependence of free energy barrier height for phenyl ring rotations in polystyrene based on non-equilibrium molecular dynamics simulations

Polystyrene properties are influenced by ring motions in side groups. The main chain conformation and interaction with the surroundings dominate the ring rotations. It is known that shear flow affects linear chain conformation and molecular distribution. However, shear-induced variations in the ring rotations have yet to be studied. This study presents a shear flow system of polystyrene via non-equilibrium molecular dynamics simulations. The free energy barrier of the phenyl ring rotations was obtained from the distribution of angle χ between the ring and main chain based on the Boltzmann distribution law. The results showed that the barrier height approaches a constant value at a shear rate less than 10¹⁰ s^? 1, but decreases with an increase in shear rate higher than 10^10.5 s^? 1. Furthermore, the radial distribution function and potential energies were compared. Remarkably, the shear flow reduced the bond vibrations of the phenyl rings, but increased the separation between intermolecular particles. Hence, a smaller cavity is necessary for the rings to rotate once but more volume is occupied by the rings. The smaller volume obtained via main chain motions needed to construct the cavity lowers the energy barrier height at shear rate higher than 10^10.5 s^? 1.     

Nanoindentation response of nickel surface using molecular dynamics simulation

The mechanisms of dislocation nucleation on a nickel (Ni) (001) surface under nanoindentation behaviours are investigated using molecular dynamics simulation. The characteristic mechanisms include the molecular models of a thermal layer (TL) and thermal with a free layer (TFL), multi-step load/unload cycles, tilt angles and shapes of the indenter, and slip vectors. The model of a TL has higher reaction force than a TFL. The maximum forces of nanoindentation decrease with increasing time of the multi-step load/unload cycle. The indenter with the tilt angle has larger force to act on the molecular model than the indenter along the normal direction. The effect of the indentation shape is presented such that the conical tip has larger load force to act on the molecular model. The defects along Shockley partials on the (111) plane are produced during nanoindentation involving nucleation, glide and slip.     

A comparison of model linear chain molecules with constrained and flexible bond lengths under planar Couette and extensional flows

We compare directly under flow two commonly used coarse grained models of linear polymers, namely the flexible finitely extensible nonlinear elastic (FENE) chain, and the freely jointed tangent sphere chain, otherwise known as the freely jointed chain. The comparison is based on viscometric, structural and dynamical properties. We use non-equilibrium molecular dynamics to simulate steady-state systems under planar Couette flow and planar extensional flow. Computed properties include shear and elongational viscosities, normal stresses, radius of gyration and end-to-end distances, order parameters, alignment angles and spin angular velocities. In all computed properties we observe very little difference between the two molecular models. Therefore, the choice of either model is suitable, though there is a computational advantage in the use of the FENE model.     

Multiscale simulation studies of geometrical effects on solution transport through nanopores

Due to intrinsic properties, solid-state nanopores are widely used in nanopore technology. Different geometries (cylindrical (CY), hourglass (HG) and conical (CO)) of artificial nanopores have been fabricated and studied. Each was found to promote different transport abilities experimentally. To explore such pore effects, the combination of finite element (FE) and molecular dynamics (MD) simulations with applied electric filed (150 mV) were performed. The dimension of anion-selective protein pore was used as a nanopore template. Different pore geometries with a narrowest diameter ranging from 1.8 to 1.8 μm were studied here. Firstly, we found that the narrowest regions at a pore orifice in CO and constriction site in HG maximise water velocity and consequently control a water flow rate. Secondly, CY triggers the highest water flux, but low ion selectivity, whilst the funnel-like geometries (HG and CO) enhance the ion selectivity significantly. Both HG and CO show similar degrees of permeant flux and selectivity. The orifice and constriction site in CO and HG are the main player for selectivity and permeation control. Thirdly, the transport properties are tuneable by changing the flow direction in asymmetric CO pore. The tip-to-base flow in CO obviously promotes stronger anion selectivity than the base-to-tip one.     

Neurite development in PC12 cells cultured on nanopillars and nanopores with sizes comparable with filopodia

We investigated the effect ofnanoscale topography on neurite development in pheochromocytoma (PC12 cells) by culturing the cells on substrates having nanoscale pillars and pores with sizes comparable with filipodia. We found that cells on nanopillars and nanopores developed fewer and shorter neurites than cells on smooth substrates, and that cells on nanopores developed more and longer neurites than cells on nanopillars. These results suggest that PC12 cells were spatially aware of the difference in the nanoscale structures of the underlying substrates and responded differently in their neurite extension. This finding points to the possibility of using nanoscale topographic features to control neurite development in neurons.     

Effects of crystal orientation and aspect ratio on plastic response of aluminium nanowires under torsion

The plastic response of perfect face-centred cubic single-crystal aluminium (Al) nanowires (NWs) under torsion is studied using molecular dynamics simulations. The Al–Al interaction is described by the many-body tight-binding potential. The effects of the crystal orientation and aspect ratio of the NWs on their deformation are evaluated in terms of atomic trajectories, potential energy, a centrosymmetry parameter and the torque required for deformation. Simulation results clearly show that for NWs, regardless of crystal orientation, dislocations nucleate and propagate on the (1 1 1) close-packed plane. In a NW under torsion, dislocations begin at the surface, extend to the interior along the (1 1 1) close-packed plane and finally diffuse to the middle part. A 〈1 1 0〉-oriented NW has the lowest required torque for deformation due to the occurrence of homogeneous deformation. The mechanism of the plastic response of an Al NW depends on its crystal orientation. For a long NW, geometry instability occurs before material instability (buckling).     

Mechanical response and deformation mechanics of Type IV pili investigated using steered coarse-grained molecular dynamics simulation

Type IV pili are long filamentous structures on the surface of bacteria, which can be rapidly assembled or disassembled with pilin subunits by molecular motors. They can generate force during retraction and are involved in many bacterial functions. Steered molecular dynamics simulations with coarse-grained MARTINI models are carried out to investigate the mechanical behaviors of pili under tension. Our study is the first to report a Young's modulus of 0.80 ± 0.07 GPa and a spring constant of 1294.6 ± 116.5 kJ mol⁻¹ nm⁻² for pilus. Our results show the mechanical responses of pili are different from those described by the worm-like chain model and the van der Waal's interactions play a critical role in the mechanical responses. Moreover, the effects of pulling rates and virtual spring constants of pilus on Young's modulus are studied and two distinct morphological stages with the conformational changes appear during the extension of pilus are observed. This work provide insight into the mechanics and the deformation mechanism of pilus assembly.     

Variability in the bioluminescence response of the dinoflagellate Pyrocystis lunula

Light emission in dinoflagellates is induced by water motions. But although it is known that mechanical stimulations of these organisms trigger the bioluminescent response, the exact mechanism that involves some cell membrane excitations by fluid motions is not yet fully understood and is still controversial. We show in this experimental study that the accelerated shear flow, created by abrupt rotations of one or both co-axial cylinders of a Couette shearing chamber excites the light emission from cultured dinoflagellates Pyrocystis lunula. Following our first results published earlier that state that pure laminar shear does not excite the main bioluminescent response in dinoflagellates, our present experiments show that both shear and acceleration in the flow are needed to trigger the bioluminescent response. Besides, the probability to stimulate this bioluminescent response under acceleration and shear is deduced from the response curves. This response follows a Gaussian distribution that traduces a heterogeneity in individual cell thresholds for the stimulation of bioluminescence in a dinoflagellate population. All these results will have a repercussion in the possible applications of dinoflagellate bioluminescence in flow visualizations and measurements. Moreover, this study opens a new way in studying mechanically-induced stimulus thresholds at the cell level.     

Wrinkling and thermal conductivity of one graphene sheet under shear

Tersoff-potential - based molecular dynamics method is used to simulate wrinkling deformation of one graphene sheet under shear, and the obtained deformation is compared with analytical solutions of macro-membrane. Furthermore, thermal conductivity of the wrinkled graphene at different temperatures is calculated. It is found that (1) the wrinkling deformation of graphene sheet under shear is close to the analytical solutions of macro-membrane under shear, which implies that the solutions of macro-membrane are applicable to predict the wrinkling deformation of graphene sheets under shear; (2) the more serious the wrinkling of the graphene under shear is, the stronger the phonon scattering is and, therefore, the lower the thermal conductivity of the wrinkled graphene is; (3) within the temperature range of 400–700 K, the thermal conductivity of graphene sheet decreases with increase in temperature.     

Molecular dynamics simulations indicate that deoxyhemoglobin,oxyhemoglobin, carboxyhemoglobin,and glycated hemoglobin under compression and shear exhibit an anisotropic mechanical behavior

We developed a new mechanical model for determining the compression and shear mechanical behavior of four different hemoglobin structures. Previous studies on hemoglobin structures have focused primarily on overall mechanical behavior; however, this study investigates the mechanical behavior of hemoglobin, a major constituent of red blood cells, using steered molecular dynamics (SMD) simulations to obtain anisotropic mechanical behavior under compression and shear loading conditions. Four different configurations of hemoglobin molecules were considered: deoxyhemoglobin (deoxyHb), oxyhemoglobin (HbO₂), carboxyhemoglobin (HbCO), and glycated hemoglobin (HbA_1C). The SMD simulations were performed on the hemoglobin variants to estimate their unidirectional stiffness and shear stiffness. Although hemoglobin is structurally denoted as a globular protein due to its spherical shape and secondary structure, our simulation results show a significant variation in the mechanical strength in different directions (anisotropy) and also a strength variation among the four different hemoglobin configurations studied. The glycated hemoglobin molecule possesses an overall higher compressive mechanical stiffness and shear stiffness when compared to deoxyhemoglobin, oxyhemoglobin, and carboxyhemoglobin molecules. Further results from the models indicate that the hemoglobin structures studied possess a soft outer shell and a stiff core based on stiffness.     

Methyl branch effects on rheological behaviours of short-chain polypropylene under steady shear studied via nonequilibrium molecular dynamics simulations

The rheological behaviours of the steady sheared short-chain polypropylene (PP) fluid are studied using isobaric isothermal nonequilibrium molecular dynamics simulations. By comparing the behaviours of PP fluid with that of the linear alkane fluid of n-hexadecane (C₁₆) having equal backbone length, we investigated the effects of the branch structure on shear thinning, rotational relaxation time, critical shear rate and potential energies. The results showed that the degree of shear thinning of the PP fluid is lower than that of the C₁₆ fluid. With respect to different temperatures, the degree of shear thinning of the former is less sensitive than that of the latter. At the molecular level, potential energies including van der Waals nonbonding interaction and bond stretching, bond bending, and bond torsion interactions are discussed. Significantly, the varying tendency of the bending potential of the PP fluid at very high shear rates is contrary to that of the C₁₆ fluid. We propose, therefore, that the branch structure affects the bending angle distribution such that it causes differences in the rheological behaviours of these two fluids. Furthermore, in all the molecular potentials of the PP fluid, the torsion potential of the dihedral angle is observed to be the strongest dependent upon temperature.     

Role of the switch II region in the conformational transition of activation of Ha-ras-p21

The role of the switch II region in the conformational transition of activation of Ha-ras-p21 has been investigated by mutating residues predicted to act as hinges for the conformational transition of this loop (Ala59, Gly60, and Gly75) (Díaz JF, Wroblowski B, Schlitter J, Engelborghs Y, 1997, Proteins 28:434-451), as well as mutating the catalytic residue Gln61. The proposed mutations of the hinge residues decrease the rate of the conformational transition of activation as measured by the binding of BeF3- to the GDP-p21 complex. Also, the thermodynamic parameters of the binding reaction are altered by a factor between three and five, depending on the temperature. (Due to changes in activation and reaction enthalpies, partially compensated by entropy changes.) The control mutation Q61H in which only the catalytic residue is changed has only a limited effect on the kinetic rate constants of the conformational transition and on the thermodynamic parameters of the reaction. The fact that mutations of the hinge residues of the switch II region affect both the binding of the phosphate analog and the conformational transition of activation indicates that the switch II is implicated both in the early and the late states of the transition.     

Local segmental dynamics of cis-1,4-polybutadiene,polypropylene and polyethylene terephthalate via molecular dynamics simulations

The local segmental dynamics of cis-1,4-polybutadiene, polypropylene and polyethylene terephthalate have been investigated via isothermal-isobaric molecular dynamics simulations. The simulation pressure was 1 atm for all systems, with all simulation temperatures being at least 150 K above the polymer's glass transition temperature. The trajectories have been analysed via autocorrelation functions (ACFs) of chord vectors spanning different number of chain backbone bonds. Inverse Laplace transformations of these ACFs using the CONTIN algorithm afforded the corresponding distribution of relaxation times (DRTs) for the simulated dynamics. All DRTs illustrated a peak on fast timescales corresponding to short length scale segmental motion and a peak at longer timescales corresponding to longer length scale relaxations. A third peak, intermediate between the fast and slow processes, appears as the relaxation of chord vectors spanning increasing number of backbone bonds is considered. The temperature dependence of the relaxation dynamics is also investigated.     

植物对它类生物应答反应的研究现状及展望

植物在与它类生物长期协同进化的过程中以及遭受它类生物的攻击时形成了一套完整的防御体系以减轻外界对其造成的伤害。从接受取食伤害和病原体侵染等外源信号,到水杨酸、茉莉酸、乙烯等一系列内源信号的传导以及应答反应的调控,再到各种生理生化表现,植物对它类生物的应答反应经历了错综复杂的过程。随着现代分子生物技术的不断进步,相关生理生化研究不断完善,植物应答反应分子机制将不断明晰,并逐步应用于植物保护,以及植物、昆虫和微生物的相互关系分析。     

Induction of mammalian cell death by simple shear and extensional flows

In this work we investigated whether the type of shear flow, to which cells are exposed, influences the initiation of cell death. It is shown that mammalian cells, indeed, distinguish between discrete types of flow and respond differently. Two flow devices were employed to impose accurate hydrodynamic flow fields: uniform steady simple shear flow and oscillating extensional flow. To distinguish between necrotic and apoptotic cell death, fluorescence activated cell sorting and the release of DNA in the culture supernatant was used. Results show that Chinese Hamster Ovaries and Human Embryonic Kidney cells will enter the apoptotic pathway when subjected to low levels of hydrodynamic stress (around 2.0 Pa) in oscillating, extensional flow. In contrast, necrotic death prevails when the cells are exposed to hydrodynamic stresses around 1.0 Pa in simple shear flow or around 500 Pa in extensional flow. These threshold values at which cells enter the respective death pathway should be avoided when culturing cells for recombinant protein production to enhance culture longevity and productivity. Biotechnol. Bioeng. 2009; 104: 360–370 © 2009 Wiley Periodicals, Inc.