Cell penetrating peptides (CPPs) are short peptides that can carry biomolecules of varying sizes across the cell membrane into the cytoplasm. Correctly identifying CPPs is the basis for studying their functions and mechanisms. Here, we propose a novel CPP predictor that is able to predict CPPs and their uptake efficiency. In our method, five feature descriptors are applied to encode the sequence and compose a hybrid feature vector. Afterward, the wrapper + random forest algorithm is employed, which combines feature selection with the prediction process to find features that are crucial for identifying CPPs. The jackknife cross validation result shows that our predictor is comparable to state-of-the-art CPP predictors, and our method reduces the feature dimension, which improves computational efficiency and avoids overfitting, allowing our predictor to be adopted to identify large-scale CPP data.
We review theories of polyelectrolyte (PE) coacervation, which is the spontaneous association of oppositely charged units of PEs and phase separation into a polymer-dense phase in aqueous solution. The simplest theories can be divided into “physics-based” and “chemistry-based” approaches. In the former, polyelectrolytes are treated as charged, long-chain, molecules, defined by charge level, chain length, and chain flexibility, but otherwise lacking chemical identity, with electrostatic interactions driving coacervation. The “chemistry-based” approaches focus on the local interactions between the species for which chemical identity is critical, and describe coacervation as the result of competitive local binding interactions of monomers and salts. In this article, we show how these approaches complement each other by presenting recent approaches that take both physical and chemical effects into account. Finally, we suggest future directions towards producing theories that are made quantitatively predictive by accounting for both long range electrostatic and local chemically specific interactions.
The temporal analysis of products (TAP) reactor provides a route to extract intrinsic kinetics from transient measurements. Current TAP uncertainty quantification only considers the experimental noise present in the outlet flow signal. Additional sources of uncertainty such as initial surface coverages, catalyst zone location, inert void fraction, gas pulse intensity and pulse delay, are not included. For this reason, a framework for quantifying initial state uncertainties present in TAP experiments is presented and applied to a carbon monoxide oxidation case study. Two methods for quantifying these sources of uncertainty are introduced. The first utilizes initial state sensitivities to approximate the parameter variances and provide insights into the structural certainty of the model. The second generates parameter confidence distributions through an ensemble-based sampling algorithm. The initial state covariance matrix can ultimately be merged with the experimental noise covariance matrix, providing a unified description of the parameter uncertainties for a TAP experiment.
Fe-Ni materials with varying Ni loading are developed for separate H2 and CO production by CH4-CO2 chemical looping. The product streams are obtained by first feeding CH4, which decomposes to H2 and carbon. The latter acts as reductant for the subsequent CO2 feed, which together with Fe re-oxidation yields CO. After 25 CH4-CO2 cycles, 10Fe5Ni@Zr has a higher H2 space-time-yield than 10Fe0Ni@Zr (〖20mmol∙s〗^(-1)∙kg_(Fe+Ni)^(-1) vs. 〖15mmol∙s〗^(-1)∙kg_(Fe+Ni)^(-1)), a 2.6 times higher CO (〖57mmol∙s〗^(-1)∙kg_(Fe+Ni)^(-1)) and lower deactivation. This improvement has two reasons: (i) CH4 activation over Ni leading to cracking, (ii) product hydrogen causing deeper FeO reduction. Deactivation follows from accumulated carbon, non-reactive for CO2. On Ni and Fe sites, carbon can be removed by lattice oxygen or CO2, yielding more CO compared to the theoretical value for Fe oxidation. However, carbon that migrates away from the metals requires oxygen for removal, which restores the activity of the Ni-containing samples.
Homogeneous hydrogen transfer reactions of methacrolein (MAL) and isopropanol (IPA) to methallyl alcohol (MAA) were investigated in batch reactor (Conv.89%, Select 93.1%) and tubular reactor (Conv.88.1%, Select 95%) using aluminum isopropoxide (Al(OPri)3) as catalyst. Kinetic experiments on hydrogen transfer reactions and reaction order were investigated in batch reactor and tubular reactor. Response surface methodology (RAM) was applied to optimize the optimum reaction conditions of hydrogen transfer reaction. Purification process of MAA from product mixture after hydrogen transfer reaction was simulated with Aspen Plus software, theoretical stages, reflux ratio and feed stage of distillation tower were optimized. Density Functional Theory (DFT) was used to investigate viable reaction pathway and to probe the catalytic mechanism between reactants and catalyst, including dehydrogenation, coupling and hydrogenation reaction. Microscopic mechanisms of hydrogen transfer reaction from MAA to MAL were acquired in detail and could be easily extended to other series of hydrogen transfer reaction.
In order to address the challenge of pressure swing adsorption system optimization, an optimization framework based on pseudo transient continuation method was used and vacuum rapid pressure swing adsorption process for oxygen production as a typical example. A pseudo transient model library was established and a robust two-stage dynamic tearing model was proposed to deal with the cyclic steady state conditions. Furthermore, the time constants were discussed and a practical time constant strategy and expressions were proposed for the stability and efficiency of calculation. Finally, reduced successive quadratic programming and time relaxation algorithm were used for the optimization of the two systems respectively, and the optimization results showed that although the simulation time of pseudo transient system is slightly higher than that of single discretization system, the optimization expense of single discretization system in two cases were 5.7 times and 11.6 times of that of pseudo transient system respectively.
A bubble coalescence model for a solution with a nonionic surfactant and with a small bubble approach velocity was developed, in which the mechanism of how coalescence is hindered by Marangoni stress was quantitatively analyzed. The bubble coalescence time calculated for ethanol-water and MIBC-water systems were in good agreement with experimental data. At low surfactant concentrations, the Marangoni stress and bubble coalescence time increased with bulk concentration increase. Conversely, in the high concentration range, the Marangoni stress and coalescence time decreased with bulk concentration. Numerical results showed that the nonlinear relationship between coalescence time and surfactant concentration is determined by the mass transport flux between the film and its interface, which tends to diminish the spatial concentration variation of the interface, i.e., it acts as a “damper”. This damping effect increases with increased surfactant concentration, therefore decreasing the coalescence time at high concentrations.
The famous two-balloon experiment involves two identical balloons filled up with air and connected via a hollow tube, and upon onsetting the experiment one of the balloons shrinks and the other expands. Here, we present the liquid version of that experiment. We use superhydrophobic (SHP) substrates to form spherical droplets and connect them with a capillary channel. Different droplet sizes, substrates of different hydrophobicities, and various channel pathways are investigated, and morphometric parameters of the droplets are measured through image processing. In the case of SHP substrates the pumping is from the smaller droplet to the larger one, similar to the two-balloon experiment. However, if one or both of the droplets are positioned on a normal substrate the curvature radius will indicate the direction of pumping. We interpret the results by considering the Laplace pressures and the surface tension applied by the channel at the connecting points.
Experimental results on pressure drop and gas hold-up for gas-liquid flow through packed beds obtained from a second flight on the International Space Station are presented and analyzed. It is found that the gas hold-up is a function of the bed history at low liquid and gas flow rates whereas higher gas hold-up and pressure gradients are observed for the test conditions following a liquid only pre-flow compared to the test conditions following a gas only pre-flow period. Over the range of flow rates tested, the capillary force is the dominant contributor to the pressure gradient and is found to be linear with the superficial liquid velocity but is a much weaker function of the superficial gas velocity. The capillary contribution is also a function of the particle size and varies approximately inversely with the particle diameter within the range of the test conditions.
A three-dimensional, non-isothermal and multiphase model of high temperature proton exchange membrane fuel cells is built to investigate water and phosphoric acid transportation, in which a spherical agglomerate model considering catalyst layer structure and liquid phase fraction is applied to determine the electrochemical kinetics in the cathode catalyst layer. Experimental polarization curve, water proportion in the anode outlet gas and phosphoric acid distribution are selected for validation. It is found that the simulated results can represent the experimental data with reasonable accuracy. Based on the model, the effects of current density and stoichiometry on the variable distributions are analyzed. The results show that water in anode is mainly from cathode by concentration diffusion of liquid water. A higher current density leads to a greater electro-migration of phosphoric acid from cathode to anode and a higher liquid phase fraction in anode,while a lower phosphoric acid concentration in the fuel cells.
Toluene diisocyanate (TDI) is an important chemical intermediate prepared by phosgenation reaction between toluene diamine and phosgene with two steps name cold and thermal phosgenation respectively. In this paper, the reactive distillation model for the thermal phosgenation reaction based the kinetics equations was established for an industrial installation, and the effects of the different parameters on the process performance were studied firstly; then based on the analysis results, a thermal coupling process between the towers of reactive distillation and phosgene purification was presented and investigated; finally, the optimal operation scheme was simulated and the results showed that the proposed process can save the heat and cold energy with 7.29% and 32.78%, respectively, and reduce the total annual cost about 17.11%. The result of the paper can be used to guide the operation configuration or the revampment of the TDI production equipment.
Decoupling and understanding the various mass, charge and heat transport phenomena involved in the electrocatalytic transformation of small molecules (i.e. CO2, CO, H2, N2, NH3, O2, CH4) is challenging but it can be readily achieved using dimensionless quantities (i.e. Reynolds, Sherwood, Schmidt, Damköhler, Nusselt, Prandtl, and Peclet Numbers) to simplify the characterization of systems with multiple interacting physical phenomena. Herein we report the development of a gastight rotating cylinder electrode cell with well-defined mass transport characteristics that can be applied to experimentally decouple mass transfer effects from intrinsic kinetics in electrocatalytic systems. The gastight rotating cylinder electrode cell enables the dimensionless analysis of electrocatalytic systems and should enable the rigorous research and development of electrocatalytic technologies.
The ZIF-8@Agmim core-shell hybrid material was synthesized via a favorable post-modification method of ion exchange (PMIE). This infrequent ZIF-8@Agmim core-shell structure maintains a well- integrated pore size that is almost the same as ZIF-8. The similar equilibrium isotherms with ZIF-8 and better kinetic separation towards propylene/propane than ZIF-8 render ZIF-8@Agmim to be an interesting candidate for propylene/propane separation. The core-shell hybrid nanomaterial was further used as nanofillers in the polymer of intrinsic microporosity matrix (PIM-1) for propylene/propane separation. The resultant MMMs exhibited a simultaneous increase in C3H6 permeability and C3H6/C3H8 ideal selectivity compared to pure polymer membrane owing to a synergistic effect of molecular sieving from ZIF-8 and π-complexation of Ag+ with propylene. The separation performance of the prepared MMM surpasses the upper bound line of polymer membranes. Furthermore, the hybrid materials possess superb photochemical stability and the corresponding MMMs exhibit excellent anti-aging property and long-term stability.
The recent revolution in shale gas has presented opportunities for distributed manufacturing of key commodity chemicals, such as methanol, from methane. However, the conventional methane-to-methanol process is energy intensive which negatively affects the profitability and sustainability. We report an intensified process configuration that is both economically attractive and environmentally sustainable. This flowsheet is systematically discovered using the building block-based representation and optimization methodology. The new process configuration utilizes membrane-assisted reactive separations and can have as much as 190% higher total annual profit compared to a conventional configuration. Additionally, it has 57% less CO2-equivalent greenhouse gas (GHG) emission. Such drastic improvement highlights the advantages of building block-based computer-aided process intensification method.
A recently published approach for modeling the cross flow in an extruder channel using a new solution to the biharmonic equation is utilized in a study of chaotic mixing in a free helix single screw extruder. This novel extruder was designed and constructed with the screw flight, also referred to as the helix, detached from the screw core. Each of the screw elements could be rotated independently to obtain chaotic motion in the screw channel. Using the new extruder, experimental evidence for the increased mixing of a dye, for both a Dirac and droplet input, with a chaotic flow field relative to the traditional residence time distribution is presented. These experimental results are compared using the new biharmonic equation-based model. Because of the ability to periodically rotate only the flight/helix, the chaotic mixing results are minimally confounded by the existence of Moffat eddies.
Process synthesis using rigorous unit operation models is highly desirable to identify the most efficient pathway for sustainable production of fuels and value-added chemicals. However, it often leads to a large-scale strongly nonlinear and nonconvex mixed integer nonlinear programming (MINLP) model. In this work, we propose two robust homotopy continuation enhanced branch and bound (HCBB) algorithms (denoted as HCBB-FP and HCBB-RB) where the homotopy continuation method is employed to gradually approach the optimal solution of the NLP subproblem at a node from the solution at its parent node. A variable step length is adapted to effectively balance feasibility and computational efficiency. The computational results demonstrate that the proposed HCBB algorithms can find the same optimal solution from different initial points, while the existing MINLP algorithms fail or find much worse solutions. In addition, HCBB-RB is superior to HCBB-FP due to lower computational effort required for the same locally optimal solution.
A novel adaptive refined grid search strategy is developed for representative characterization of process feasible region boundaries and accurate estimation of its hypervolume. In particular, a linked list data structure adopted from the field of computer science is used to maintain the grid connectivity information. A uniform perturbation scheme is used to refine the search only near boundaries. The volumetric flexibility index FI_V is calculated directly from a summation of feasible hypercubes in the grid, without the need to apply shape reconstruction techniques. The proposed adaptive grid search strategy can capture complex region shapes with reduced sampling costs and without randomness for better reproducibility. Operational flexibility is optimized traditionally at a process scale. A case study on refrigerant selection is presented to demonstrated that the developed strategy could be combined within a computer-aided molecular design framework for operational flexibility optimization in molecular scale.
In this study, a CFD mathematical model has been developed for catalytic fast pyrolysis (CFP) of biomass. The multi-phase fluid flow, and the inter-phase momentum and energy transfer processes were modelled with Eulerian multi-phase formulas. The biomass catalyst fast pyrolysis reactions were described by using a two-stage, semi-global model. Specified secondary tar catalytic cracking process, which considers both intrinsic reaction rates and mass transfer process are embedded to the developed model by user-defined function (UDF). The developed model has then been employed to investigate the effects of structural properties of catalyst, such as specific internal area, average size of active sites, pore diameter, and tortuosity, on products yields and composition. The influences of adsorption capability of tar molecule on catalyst surface and external film mass transfer were also analyzed. The developed model can be employed for further research and engineering designs of the catalyst pyrolysis of carbonaceous materials.