Enhanced sampling for lipid-protein interactions during membrane dynamics

The inflexible concept of membrane curvature as an independent property of lipid structures is today obsolete.Lipid bilayers behave as many-body entities with emergent properties that depend on their interactions with the environment.In particular,proteins exert crucial actions on lipid molecules that ultimately condition the collective properties of the membranes.In this review,the potential of enhanced molecular dynamics to address cell-biology problems is discussed.The cases of membrane deformation,membrane fusion,and the fusion pore are analyzed from the perspective of the dimensionality reduction by collective variables.Coupled lipid-protein interactions as fundamental determinants of large membrane remodeling events are also commented.Finally,novel strategies merging cell biology and physics are considered as future lines of research.

Coarse grained molecular dynamics and theoretical studies of carbon nanotubes entering cell membrane

Motivated by recent experimental observations that carbon nanotubes （CNT） can enter animal cells, here we conduct coarse grained molecular dynamics and theoretical studies of the intrinsic interaction mechanisms between CNT＇s and lipid bilayer. The results indicate that CNT-cell interaction is dominated by van der Waals and hydrophobic forces, and that CNT＇s with sufficiently small radii can directly pierce through cell membrane while larger tubes tend to enter cell via a wrapping mechanism. Theoretical models are proposed to explain the observed size effect in transition of entry mechanisms.

Analysis of pH-dependent Structure and Mass Transfer Characteristics of Polydopamine Membranes by Molecular Dynamics Simulation

Detailed atomistic structures are constructed for polydopamine membranes containing different amounts of catechol and quinone groups to investigate the effect of p H value in the membrane casting solution on sorption and diffusion of small gas molecules(water and propylene) in the membranes. Interactions between dopamine oligomers are calculated, and it is found that the interactions decrease from- 2356.52 k J·mol-1in DOP-1 to-1586.69 k J·mol-1in DOP-3 when all of the catechol groups are converted to quinone groups. The mobility of polymer segments and free volume properties of polydopamine membranes are analyzed. The sorption quantities of water and propylene in the membrane are calculated using Grand Canonical Monte Carlo method. The sorption results show that water adsorbed in DOP-1, DOP-2 and DOP-3 are 17.3, 18.6 and 20.0 mg water per gram polymer, respectively, and no propylene molecule can be adsorbed. The diffusion behavior of water molecules in the membrane is investigated by molecular dynamics simulation. The diffusion coefficients of water molecules in DOP-1, DOP-2 and DOP-3 membranes are(1.80 ± 0.52) × 10-11,(3.40 ± 0.64) × 10-11and(4.50 ± 0.92) × 10-11m2·s-1, respectively. The predicted sorption quantities and diffusion coefficients of water and propylene in the membrane present the same trends as those from experimental results.

Fouling process and anti-fouling mechanisms of dynamic membrane assisted by photocatalytic oxidation under sub-critical fluxes

Membrane fouling is often considered as a hindrance for the application of microfiltration/ultrafiltration(MF/UF) for drinking water production. A novel process of photocatalytic membrane reactor/dynamic membrane(PMR/DM), operating in a continuous mode under sub-critical flux, was proposed for the mitigation of membrane fouling caused by humic acids(HAs) in water. The mechanism of membrane fouling alleviation with synergistic photocatalytic oxidation and dynamic layer isolating effect was comprehensively investigated from the characterization of foulant evolution responsible for the reversible and irreversible fouling. The results showed that the PMR/DM utilized photocatalytic oxidation to enhance the porosity and hydrophilicity of the fouling layer by converting the high molecular weight(MW) and hydrophobic HA molecules with carboxylic functional groups and aromatic structures into low-MW hydrophilic or transphilic fractions, including tryptophan-like or fulvic-like substances. The fouling layer formed in the PMR/DM by combination of photocatalytic oxidation and DM running at a sub-critical flux of 100 L·h^-1·m^-2, was more hydrophilic and more porous, resulting in the lowest trans-membrane pressure(TMP) growth rates, as compared to the processes of ceramic membrane(CM), DM and PMR/CM.Meanwhile, the dynamic layer prevented the foulants, particularly the high-MW hydrophobic fractions,from contacting the primary membrane, which enabled the membrane permeability to be restored easily.

ANALYSIS OF THE LARGE DEFLECTION DYNAMIC PLASTIC RESPONSE OF SIMPLY-SUPPORTED CIRCULAR PLATES BY THE“MEMBRANE FACTOR METHOD”

Based on energy equilibrium,a new procedure called the Membrane Factor Method is devel- oped to analyze the dynamic plastic response of plates with deflections in the range where both bending mo- ments and membrane forces are important.The final deflection of a simply -supported circular rigid-plastic plate loaded by a uniformly distributed impulse is obtained.In comparison with other approximate solutions, the present results are found to be simpler and in better agreement with the corresponding experimental values reoorded by Florence.

Dynamic Thermal Model and Temperature Control of Proton Exchange Membrane Fuel Cell Stack

A dynamic thermal transfer model of a proton exchange membrane fuel cell (PEMFC) stack is developed based on energy conservation in order to reach better temperature control of PEMFC stack. Considering its uncertain parameters and disturbance, we propose a robust adaptive controller based on backstepping algorithm of Lyaponov function. Numerical simulations indicate the validity of the proposed controller.

Theoretical Study on Dynamic Filtration with the Membrane in Simple Harmonic Motion

A simple harmonic motion is proposed to make the membrane move in a simpleharmonic way so as to enhance the membrane filtration, and minimize the membrane fouling andconcentration polarization. The velocity distribution and pressure distribution are deduced from theNavier-Stokes equation on the basis of a laminar flow when the membrane rotates at the speed of Asin(αt). And then the shear stress, shear force, moment of force on the membrane surface and powerconsumed by viscous force are calculated. The velocity distribution demonstrates that the phase ofmembrane velocity does not synchronize with that of shear stress. The simple harmonic motion canresult in self-cleaning, optimize energy utilization, provide the velocity field with instability,and make the feed fluid fluctuation. It also results in higher shear stress on the membrane surfacethan the constant motion when they consume the same quantitative energy.

Mass Transfer, Gas Holdup, and Kinetic Models of Batch and Continuous Fermentation in a Novel Rectangular Dynamic Membrane Airlift Bioreactor

Compared with conventional cylinder airlift bioreactors(CCABs)that produce coarse bubbles,a novel rectangular dynamic membrane airlift bioreactor(RDMAB)developed in our lab produces fine bubbles to enhance the volumetric oxygen mass transfer coefficient(k_(L)a)and gas holdup,as well as improve the bioprocess in a bioreactor.In this study,we compared mass transfer,gas holdup,and batch and con-tinuous fermentation for RNA production in CCAB and RDMAB.In addition,unstructured kinetic models for microbial growth,substrate utilization,and RNA formation were established.In batch fermentation,biomass,RNA yield,and substrate utilization in the RDMAB were higher than those in the CCAB,which indicates that dynamic membrane aeration produced a high k_(L)a by fine bubbles;a higher k_(L)a is more bene-ficial to aerobic fermentation.The starting time of continuous fermentation in the RDMAB was 20 h ear-lier than that in the CCAB,which greatly improved the biological process.During continuous fermentation,maintaining the same dissolved oxygen level and a constant dilution rate,the biomass accumulation and RNA concentration in the RDMAB were 9.71% and 11.15% higher than those in the CCAB,respectively.Finally,the dilution rate of RDMAB was 16.7% higher than that of CCAB during con-tinuous fermentation while maintaining the same air aeration.In summary,RDMAB is more suitable for continuous fermentation processes.Developing new aeration and structural geometry in airlift bioreac-tors to enhance k_(L)a and gas holdup is becoming increasingly important to improve bioprocesses in a bioreactor.

Studies on the Response Dynamics of a Gas-Sensing Membrane Probe

The present paper covers the response dynamics of a gas-sensing membrane probe, which is described by the dynamic differential equation based upon a steady-state diffusion process. The theoretical results indicate that the response time is dependent upon membrane properties, membrane geometry, internal electrolyte composition, the dissociation constant of the conjugate reaction, the initial gas concentration in the internal electrolyte, and the gas concentration in the evaluation sample. The theoretical prediction is in good agreement with the experimental result. A method for determining a gas-sensing probe' s dynamic parameter is proposed in this paper also.

Multiscale molecular dynamics simulations of membrane remodeling by Bin/Amphiphysin/Rvs family proteins

Membrane curvature is no longer thought of as a passive property of the membrane; rather, it is considered as an ac- tive, regulated state that serves various purposes in the cell such as between cells and organelle definition. While transport is usually mediated by tiny membrane bubbles known as vesicles or membrane tubules, such communication requires complex interplay between the lipid bilayers and cytosolic proteins such as members of the Bin/Amphiphysin/Rvs （BAR） superfam- ily of proteins. With rapid developments in novel experimental techniques, membrane remodeling has become a rapidly emerging new field in recent years. Molecular dynamics （MD） simulations are important tools for obtaining atomistic information regarding the structural and dynamic aspects of biological systems and for understanding the physics-related aspects. The availability of more sophisticated experimental data poses challenges to the theoretical community for devel- oping novel theoretical and computational techniques that can be used to better interpret the experimental results to obtain further functional insights. In this review, we summarize the general mechanisms underlying membrane remodeling con- trolled or mediated by proteins. While studies combining experiments and molecular dynamics simulations recall existing mechanistic models, concurrently, they extend the role of different BAR domain proteins during membrane remodeling pro- cesses. We review these recent findings, focusing on how multiscale molecular dynamics simulations aid in understanding the physical basis of BAR domain proteins, as a representative of membrane-remodeling proteins.

Dynamic modeling of a H_2O-permselective membrane reactor to enhance methanol synthesis from syngas considering catalyst deactivation

In this paper, the effect of water vapor removal on methanol synthesis capacity from syngas in a fixed-bed membrane reactor is studied considering long-term catalyst deactivation. A dynamic heterogeneous one-dimensional mathematical model that is composed of two sides is developed to predict the performance of this configuration. In this configuration, conventional methanol reactor is supported by an aluminasilica composite membrane layer for water vapor removal from reaction zone. To verify the accuracy of the considered model and assumptions, simulation results of the conventional methanol reactor is compared with the industrial plant data under the same process condition. The membrane reactor improves catalyst life time and enhances CO2 conversion to methanol by overcoming the limitation imposed by thermodynamic equilibrium. This configuration has enhanced the methanol production capacity about 4.06% compared with the industrial methanol reactor during the production time.

Non-equilibrium Thermodynamic Analysis of The Transport Properties of Formed-in-Place Zirconium (Ⅳ) Hydrous Oxide-Polyacylate Membranes in aqueous NaNO_3 solution

Nanofiltration of aqueous NaNO3 solution with a dynamically formed Zr(IV) hydrousoxide-PAA membrane is presented. The practical transpoft coefficients Lp, σ, ω were obtainedusing relationships of the non-equilibrium thermodynamics and were used to calculate thefrictional coefficients of a friction model.

Some qualitative properties of incompressible hyperelastic spherical membranes under dynamic loads

Some nonlinear dynamic properties of axisymmetric deformation are ex- amined for a spherical membrane composed of a transversely isotropic incompressible Rivlin-Saunders material. The membrane is subjected to periodic step loads at its inner and outer surfaces. A second-order nonlinear ordinary differential equation approximately describing radially symmetric motion of the membrane is obtained by setting the thick- ness of the spherical structure close to one. The qualitative properties of the solutions are discussed in detail. In particular, the conditions that control the nonlinear periodic oscillation of the spherical membrane are proposed. In certain cases, it is proved that the oscillating form of the spherical membrane would present a homoclinic orbit of type ＂∞＂, and the amplitude growth of the periodic oscillation is discontinuous. Numerical results are provided.

Solid-State NMR Spectroscopic Approaches to Investigate Dynamics, Secondary Structure and Topology of Membrane Proteins

Solid-state NMR spectroscopy is routinely used to determine the structural and dynamic properties of both membrane proteins and peptides in phospholipid bilayers [1-26]. From the perspective of the perpetuated lipids, 2H solid-state NMR spectroscopy can be used to probe the effect of embedded proteins on the order and dynamics of the acyl chains of phospholipid bilayers [8-13]. Moreover, 31P solid-state NMR spectroscopy can be used to investigate the interaction of peptides, proteins and drugs with phospholipid head groups [11-14]. The secondary structure of 13C = O site-specific isotopically labeled peptides or proteins inserted into lipid bilayers can be probed utilizing 13C CPMAS solid-state NMR spectroscopy [15-18]. Also, solid-state NMR spectroscopic studies can be utilized to ascertain pertinent informa- tion on the backbone and side-chain dynamics of 2H- and 15N-labeled proteins, respectively, in phospholipid bilayers [19-26]. Finally, specific 15N-labeled amide sites on a protein embedded inside oriented bilayers can be used to probe the alignment of the helices with respect to the bilayer normal [2]. A brief summary of all these solid-state NMR ap- proaches are provided in this minireview.

Multinanoparticle Translocations in Phospholipid Membranes:Translocation Modes and Dynamic Processes

Multinanoparticles interacting with the phospholipid membranes in solution were studied by dissipative particle dynamics simulation.The selected nanoparticles have spherical or cylindrical shapes,and they have various initial velocities in the dynamical processes.Several translocation modes are defined according to their characteristics in the dynamical processes,in which the phase diagrams are constructed based on the interaction strengths between the particles and membranes and the initial velocities of particles.Furthermore,several parameters,such as the system energy and radius of gyration,are investigated in the dynamical processes for the various translocation modes.Results elucidate the effects of multiparticles interacting with the membranes in the biological processes.

The effect of ZIF-90 particle in Pebax/Psf composite membrane on the transport properties of CO2,CH4 and N2 gases by Molecular Dynamics Simulation method

Nowadays,mixed matrix membranes(MMMs)have considered by many researchers to overcome the problems of polymeric membranes.In addition,molecular dynamics(MD)and Monte Carlo(MC)simulation Methods are suitable tools for studying transport properties and morphology in MMMs.For this purpose,in this study using material studio 2017(MS)software,the transport properties of CO2,CH4 and N2 in Pebax,Psf neat Pebax/Psf composite and Pebax/Psf composite filled with ZIF-90 particles have been investigated.By adding Psf to Pebax matrix,the selectivity of CO2/CH4 and CO2/N2 gases has significantly increased.In addition,adding ZIF-90 particles to the Pebax/Psf composite increased the permeability of CO2,CH4 and N2 compared to neat and composite membranes.The morphological properties of the membranes,such as the fractional free volume(FFV),radial distribution function(RDF),glass transition temperature(TG),X-ray diffraction(XRD)and equilibrium density have calculated and acceptable results have obtained.

Dynamic Membrane for Cross-flow Micro-filtration in Treating Activated Sludge

Mixed liquid of activated sludge (AS) were micro-filtrated by dynamic membrane (DM) made of 6000 mesh kaolin. The results illustrated that the permeate quality and flux with DM filtration were superior to that with direct filtration in treating AS. The experiments of membrane washing showed that DM could abate the internal fouling of membranes efficiently, and the permeate flux of renewed membrane reached 90% of that of new membranes. The denser the mixed liquid suspended solids (MLSS) were, the lower the permeate flux was. Increasing of both flow velocity over the membrane surface and trans-membrane pressure (TMP) could lead to some enhancement of permeate flux, while the former approach could be carried out more economically. The feasibility of application of the DM to membrane bioreactor (MBR) has been ascertained.

Analysis on nonlinear wind-induced dynamic response of membrane roofs with aerodynamic effects

Based on the characteristics of membrane structures and the air influence factors,this paper presented a method to simulate the air aerodynamic force effects including the added air mass,the acoustic radiation damping and the pneumatic stiffness.The infinite air was modeled using the acoustic fluid element of commercial FE software and the finite element membrane roof models were coupled with fluid models.A comparison between the results obtained by FE computation and those obtained by the vibration experiment for a cable-membrane verified the validity of the method.Furthermore,applying the method to a flat membrane roof structure and using its wind tunnel test results,the analysis of nonlinear wind-induced dynamic responses for such geometrically nonlinear roofs,including the roof-air coupled model was performed.The result shows that the air has large influence on vibrating membrane roofs according to results of comparing the nodal time-history displacements,accelerations and stress of the two different cases.Meantime,numerical studies show that the method developed can successfully solve the nonlinear wind-induced dynamic response of the membrane roof with aerodynamic effects.

Different efficiency toward the biomimetic aerobic oxidation of benzyl alcohol in microchannel and bubble column reactors: Hydrodynamic characteristics and gas–liquid mass transfer

The selective aerobic oxidation of benzyl alcohol to benzaldehyde has attracted considerable attention because benzaldehyde is a high value-added product. The rate of this typical gas–liquid reaction is significantly affected by mass transfer. In this study, CoTPP-mediated(CoTPP: cobalt(II) mesotetraphenylporphyrin) selective benzyl alcohol oxidation with oxygen was conducted in a membrane microchannel(MMC) reactor and a bubble column(BC) reactor, respectively. We observed that 83% benzyl alcohol was converted within 6.5 min in the MMC reactor, but only less than 10% benzyl alcohol was converted in the BC reactor. Hydrodynamic characteristics and gas–liquid mass transfer performances were compared for the MMC and BC reactors. The MMC reactor was assumed to be a plug flow reactor,and the dimensionless variance was 0.29. Compared to the BC reactor, the gas–liquid mass transfer was intensified significantly in MMC reactor. It could be ascribed to the high gas holdup(2.9 times higher than that of BC reactor), liquid film mass transfer coefficient(8.2 times higher than that of BC reactor), and mass transfer coefficient per unit interfacial area(3.8 times higher than that of BC reactor). Moreover,the Hatta number for the MMC reactor reached up to 0.61, which was about 15 times higher than that of the BC reactor. The computational fluid dynamics calculations for mass fractions in both liquid and gas phases were consistent with the experimental data.

Dynamic soil arching in piled embankment under train load of high-speed railways

Piled embankments have many advantages that have been applied in high-speed railway construction engineering.However,the load transfer mechanism of piled embankments,such as soil arching and tension membranes,is still unclear,especially under dynamic loads.To investigate the soil arching and tension membrane under dynamic train loads on high-speed railways,a large-scale piled embankment model test with X-shaped piles as vertical reinforcement was performed,in which twenty-eight earth pressure cells were installed in the piled embankment and an M-shaped wave was adopted to simulate the high-speed railway train load.The results show that dynamic soil arching only occurs when two bogies of a carriage pass by and disappears at other times.The dynamic soil arching and membrane effect are the most significant under the concrete base.The arching height,stress concentration ratio and pile-soil load sharing ratio have a minimal value at 25 Hz.The dynamic soil arching degrades severely at 25 Hz,whose height at 25 Hz is only 0.35 times that at 5 Hz.The arching height fluctuates over a narrow range with increasing loading amplitude.The stress concentration ratio and the pile-soil load sharing ratio increase monotonically as the loading amplitude increases.