Molecular dynamics simulation of thread break-up and formation of droplets in nanoejection system

This study investigated nanojet processes by a non-equilibrium molecular dynamics simulation. The phenomena of liquid thread break-up and droplet formation were simulated by compressing liquid propane molecules with various compressing velocities. Properties' distributions show that, at the nanoscale, density and pressure were neither uniform nor continuous during the ejection process. Shear heating phenomena were found in the contact area of the nozzle channel. A linear relationship between the length of liquid threads and the compressing velocity was also found in this study. The results from different trials using various compressing velocities show that higher compressing velocities in nanojet processes result in longer liquid thread lengths and liquid molecules with higher energy levels. Therefore, the ejection process is more unstable, resulting in an increase in the number of evaporating molecules and satellite droplets. Results that illustrate various features are presented to aid in the comprehension of the nanojet processes.     

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.     

A Cost-effective and Reliable Method to Predict Mechanical Stress in Single-use and Standard Pumps

Pumps are mainly used when transferring sterile culture broths in biopharmaceutical and biotechnological production processes. However, during the pumping process shear forces occur which can lead to qualitative and/or quantitative product loss. To calculate the mechanical stress with limited experimental expense, an oil-water emulsion system was used, whose suitability was demonstrated for drop size detections in bioreactors¹. As drop breakup of the oil-water emulsion system is a function of mechanical stress, drop sizes need to be counted over the experimental time of shear stress investigations. In previous studies, the inline endoscopy has been shown to be an accurate and reliable measurement technique for drop size detections in liquid/liquid dispersions. The aim of this protocol is to show the suitability of the inline endoscopy technique for drop size measurements in pumping processes. In order to express the drop size, the Sauter mean diameter d₃₂ was used as the representative diameter of drops in the oil-water emulsion. The results showed low variation in the Sauter mean diameters, which were quantified by standard deviations of below 15%, indicating the reliability of the measurement technique.     

Ionic liquid-based in situ product removal design exemplified for an acetone–butanol–ethanol fermentation

Selecting an appropriate separation technique is essential for the application of in situ product removal (ISPR) technology in biological processes. In this work, a three-stage systematic design method is proposed as a guide to integrate ionic liquid (IL)-based separation techniques into ISPR. This design method combines the selection of a suitable ISPR processing scheme, the optimal design of an IL-based liquid–liquid extraction (LLE) system followed by process simulation and evaluation. As a proof of concept, results for a conventional acetone–butanol–ethanol fermentation are presented (40,000 ton/year butanol production). In this application, ILs tetradecyl(trihexyl)phosphonium tetracyanoborate ([TDPh][TCB]) and tetraoctylammonium 2-methyl-1-naphthoate ([TOA] [MNaph]) are identified as the optimal solvents from computer-aided IL design (CAILD) method and reported experimental data, respectively. The dynamic simulation results for the fermentation process show that, the productivity of IL-based in situ (fed-batch) process and in situ (batch) process is around 2.7 and 1.8fold that of base case. Additionally, the IL-based in situ (fed-batch) process and in situ (batch) process also have significant energy savings (79.6% and 77.6%) when compared to the base case.     

Process and technoeconomic analysis of leading pretreatment technologies for lignocellulosic ethanol production using switchgrass

Six biomass pretreatment processes to convert switchgrass to fermentable sugars and ultimately to cellulosic ethanol are compared on a consistent basis in this technoeconomic analysis. The six pretreatment processes are ammonia fiber expansion (AFEX), dilute acid (DA), lime, liquid hot water (LHW), soaking in aqueous ammonia (SAA), and sulfur dioxide-impregnated steam explosion (SO(2)). Each pretreatment process is modeled in the framework of an existing biochemical design model so that systematic variations of process-related changes are consistently captured. The pretreatment area process design and simulation are based on the research data generated within the Biomass Refining Consortium for Applied Fundamentals and Innovation (CAFI) 3 project. Overall ethanol production, total capital investment, and minimum ethanol selling price (MESP) are reported along with selected sensitivity analysis. The results show limited differentiation between the projected economic performances of the pretreatment options, except for processes that exhibit significantly lower monomer sugar and resulting ethanol yields.     

Storage and growth of denitrifiers in aerobic granules: part I. model development

A mathematical model, based on the Activated Sludge Model No.3 (ASM3), is developed to describe the storage and growth activities of denitrifiers in aerobic granules under anoxic conditions. In this model, mass transfer, hydrolysis, simultaneous anoxic storage and growth, anoxic maintenance, and endogenous decay are all taken into account. The model established is implemented in the well-established AQUASIM simulation software. A combination of completely mixed reactor and biofilm reactor compartments provided by AQUASIM is used to simulate the mass transport and conversion processes occurring in both bulk liquid and granules. The modeling results explicitly show that the external substrate is immediately utilized for storage and growth at feast phase. More external substrates are diverted to storage process than the primary biomass production process. The model simulation indicates that the nitrate utilization rate (NUR) of granules-based denitrification process includes four linear phases of nitrate reduction. Furthermore, the methodology for determining the most important parameter in this model, that is, anoxic reduction factor, is established.     

Myxococcus xanthus mutants with temperature-sensitive, stage-specific defects: evidence for independent pathways in development.

Fruiting-body formation in the bacterium Myxococcus xanthus consists of a temporal sequence of cellular aggregation and sporulation. To examine the developmental stages more closely, we established synchronous and reproducible conditions for fruiting-body formation. Mutants that are temperature sensitive for fruiting-body formation were isolated and analyzed under these conditions. The terminal morphologies of the mutant strains at the nonpermissive temperature were found to resemble intermediate stages of fruiting-body formation and therefore were grouped in the following phenotypic classes: (i) rough mutants, which show no aggregation; (ii) swirl mutants, which show defective aggregation; (iii) flat-mound mutants and translucent-mound mutants, mutants which aggregate but show very low levels of sporulation. The mutants were characterized by temperature-shift experiments and found to exhibit discrete and reproducible temperature-sensitive periods. The ends of the temperature-sensitive periods in the various mutants covered a broad range of the developmental cycle. No correlation was found between the terminal morphologies at the restrictive temperature and the timing of the temperature-sensitive periods. However, the terminal morphologies correlated well with sporulation. The rough and swirl mutants produced normal numbers of myxospores at 34 degrees C even though they failed to aggregate. In contrast, the flat-mound and translucent-mound mutants, which aggregate normally, produced very few spores. The translucent-mound mutants were also temperature sensitive for induction of glycerol spores. The results indicate that both aggregation and sporulation are initiated early in the developmental cycle and that these processes are largely independent of each other.     

Process simulation of modified dry grind ethanol plant with recycle of pretreated and enzymatically hydrolyzed distillers' grains

Distillers' grains (DG), a co-product of a dry grind ethanol process, is an excellent source of supplemental proteins in livestock feed. Studies have shown that, due to its high polymeric sugar contents and ease of hydrolysis, the distillers' grains have potential as an additional source of fermentable sugars for ethanol fermentation. The benefit of processing the distillers' grains to extract fermentable sugars lies in an increased ethanol yield without significant modification in the current dry grind technology. Three different potential configurations of process alternatives in which pretreated and hydrolyzed distillers' grains are recycled for an enhanced overall ethanol yield are proposed and discussed in this paper based on the liquid hot water (LHW) pretreatment of distillers' grains. Possible limitations of each proposed process are also discussed. This paper presents a compositional analysis of distillers' grains, as well as a simulation of the modified dry grind processes with recycle of distillers' grains. Simulated material balances for the modified dry grind processes are established based on the base case assumptions. These balances are compared to the conventional dry grind process in terms of ethanol yield, compositions of its co-products, and accumulation of fermentation inhibitors. Results show that 14% higher ethanol yield is achievable by processing and hydrolyzing the distillers' grains for additional fermentable sugars, as compared to the conventional dry grind process. Accumulation of fermentation by-products and inhibitory components in the proposed process is predicted to be 2-5 times higher than in the conventional dry grind process. The impact of fermentation inhibitors is reviewed and discussed. The final eDDGS (enhanced dried distillers' grains) from the modified processes has 30-40% greater protein content per mass than DDGS, and its potential as a value-added process is also analyzed. While the case studies used to illustrate the process simulation are based on LHW pretreated DG, the process simulation itself provides a framework for evaluation of the impact of other pretreatments.     

Comparative study of liquefaction process and liquefied products from bamboo using different organic solvents

The effects of various solvents, including phenol, ethylene glycol (EG) and ethylene carbonate (EC), and different liquid ratios on the liquefaction of bamboo, have been studied systematically in this paper. The processes were catalyzed by hydrochloride acid at 180 °C in autoclaves for different reaction times. The results show that phenol is the optimum solvent for bamboo liquefaction with a yield up to 99%. The Fourier transform-infrared (FT-IR) analyses of the residues show that cellulose, hemicelluloses and lignin are almost decomposed when using phenol as solvent. The gel permeation chromatography (GPC) results of the liquid products show that the high molecular weight of bamboo decreases significantly to around 1800 g mol⁻¹ after liquefaction. The gas chromatography and mass spectrometry (GC–MS) analysis shows that low boiling point products of liquefied bamboo are similar regardless of the type of solvent used.     

Kinetic Monte Carlo simulation for the void defects formation in Czochralski silicon growth

The quality of silicon wafers used as substrates for microelectronic devices is measured in terms of the type, size and density of defects formed during crystal growth process. The native point defects such as vacancies and self-interstitials diffuse, react and aggregate to form intrinsic defects in the silicon wafers. We investigated the point defect behaviour using the kinetic lattice Monte Carlo (KLMC) model. The KLMC method has been applied extensively in various forms to the study of microdefects in silicon wafers. The purpose of this paper is to demonstrate the phenomena of void defect formation. The size and density of void defects are usually affected by system temperature, vacancy–vacancy reaction and vacancy–impurity reaction. In this paper, we study the temperature effect and the vacancy concentration effect. The simulation results with various temperatures are well matched with our experimental data, and the relationship between temperature and vacancy density describes well the phenomena of void defect formation. This is the first time such KLMC simulation results have been reported.     

Force generation by dynamic microtubules

The assembly and disassembly of microtubules can generate pushing and pulling forces that, together with motor proteins, contribute to the correct positioning of chromosomes, mitotic spindles and nuclei in cells. In vitro experiments combined with modeling have shed light on the intrinsic capability of dynamic microtubules to generate force, and various observations of positioning processes in cells and model systems have shown how pushing and pulling forces are used in different situations. A sophisticated set of microtubule-end-binding proteins is responsible for steering dynamic microtubules toward their cellular target and regulating the pushing and/or pulling forces that are generated once contact is established.     

Sparging and agitation-induced injury of cultured animals cells: Do cell-to-bubble interactions in the bulk liquid injure cells?

It has been established that the forces resulting from bubbles rupturing at the free air (gas)/liquid surface injure animal cells in agitated and/or sparged bioreactors. Although it has been suggested that bubble coalescence and breakup within agitated and sparged bioreactors (i.e., away from the free liquid surface) can be a source of cell injury as well, the evidence has been indirect. We have carried out experiments to examine this issue. The free air/liquid surface in a sparged and agitated bioractor was eliminated by completely filling the 2-L reactor and allowing sparged bubbles to escape through an outlet tube. Two identical bioreactors were run in parallel to make comparisons between cultures that were oxygenated via direct air sparging and the control culture in which silicone tubing was used for bubble-free oxygenation. Thus, cell damage from cell-to-bubble interactions due to processes (bubble coalescence and breakup) occurring in the bulk liquid could be isolated by eliminating damage due to bubbles rupturing at the free air/liquid surface of the bioreactor. We found that Chinese hamster ovary (CHO) cells grown in medium that does not contain shear-protecting additives can be agitated at rates up to 600 rpm without being damaged extensively by cell-to bubble interactions in the bulk of the bioreactor. We verified this using both batch and high-density perfusion cultures. We tested two impeller designs (pitched blade and Rushton) and found them not to affect cell damage under similar operational conditions. Sparger location (above vs. below the impeller) had no effect on cell damage at higher agitation rates but may affect the injury process at lower agitation intensities (here, below 250 rpm). In the absence of a headspace, we found less cell damage at higher agitation intensities (400 and 600 rpm), and we suggest that this nonintuitive finding derives from the important effect of bubble size and foam stability on the cell damage process. (c) 1996 John Wiley & Sons, Inc.     

Lipid peroxidation products mediate the formation of 8-hydroxydeoxyguanosine in DNA.

Membrane lipid peroxidation processes yield products that may react with DNA to cause oxidative modifications. We have investigated this possibility and have found that calf thymus DNA exposed to autooxidized lipids causes the formation of 8-hydroxy-2'-deoxyguanosine (8-OH-dG). 8-OH-dG formation in DNA was measured using high-pressure liquid chromatography with electrochemical detection. Methyl linolenate oxidized for different lengths of time was exposed to DNA. The amount of 8-OH-dG formed in DNA was proportional to the amount of lipid peroxidation as measured by the thiobarbituric reactive substances present. The formation of 8-OH-dG in DNA by autooxidized methyl linolenate was dependent on the presence of the transition metal ions Cu or Fe and was inhibited by various scavengers, including superoxide dismutase and catalase. This implicates the involvement of oxygen free radicals in the process. Liposomes formed from phosphatidylcholine (82%) and methyl arachidonate (18%) were peroxidized for different lengths of time and then exposed to DNA. 8-OH-dG was formed in DNA by exposure to Cu(II) and peroxidized liposomes. Under these conditions, Fe(III) was slightly less effective than Cu(II) in mediating 8-OH-dG formation. These observations clearly show that 8-OH-dG formation in DNA may result from processes that may occur during intracellular lipid peroxidation.     

Dynamic simulation of cyclic batch anaerobic digestion of cattle manure

Cyclic batch reactors with periodical feeds and extractions, are often used in cattle manure anaerobic digestion. The dynamic behavior of this type of reactor was simulated in this study. The kinetic model developed by I. Angelidaki et al. [Biotechnol. Bioeng. 42 (1993) 159], together with microbial growth kinetics, conventional material balances for an ideally cyclic batch reactor, liquid-gas interactions, and liquid phase equilibrium chemistry were used in this study. The model showed good agreement with the experimental data of R.I. Mackie and M.P. Bryant [Appl. Microbiol. Biotechnol. 43 (1995) 346], and R. Borja et al. [Chem. Eng. J. 54 (1994) B9]. The effects of hydraulic retention time (HRT), organic loading rate, reactant concentrations, feeding interval, and initial conditions such as pH and ammonia concentration on process performance can be evaluated by the dynamic model. Also simulation results show that the equilibrium conditions can be considered for CO2 distribution between liquid and gas phases, especially for processes with long retention times.     

Human cortical bone: the SiNuPrOs model

Many models that have been developed for cortical bone oversimplify much of the architectural and physical complexity. With SiNuPrOs model, a more complete approach is investigated: it is multiscale because it contains five structural levels and multi physic because it takes into account simultaneously structure (with various properties: elasticity, piezoelectricity, porous medium), fluid and mineralization process modelization. The multiscale aspect is modeled by using 18 structural parameters in a specific application of the mathematical theory of homogenization and 10 other physical parameters are necessary for the multi physic aspect. The modelization of collagen as a piezoelectric medium has needed the development of a new behaviour law allowing a better simulation of the effect of a medium considered as evolving during a mineralization process.

Then the main interest of SiNuPrOs deals with the possibility to study, at each level of the cortical architecture, either the elastic properties or the fluid motion or the piezoelectric effects or both of them. All these possibilities constitute a very large work and all this mass of information (fluid aspects, even at the nanoscopic scale, piezoelectric phenomena and simulations) will be presented in several papers. This first one is only devoted to the presentation of this model with an application to the computation of elastic properties at the macroscopic scale.

The computational methods have been packed into software also called SiNuPrOs and allowing a large number of predictive simulations corresponding to various different configurations.     

Les premières occupations humaines dans le Sud du Brésil : une vision géoarchéologique intégrée

Between ≈13,000 and 7000 BP, the territory of southern Brazil was occupied in a stable and diverse manner, with the main anthropic trace being in lithic material. Archaeological research has provided more consistent evidence of occupation in different environments and associated with different stratigraphic formation processes since the Late Pleistocene. Therefore, this paper proposes to analyse the history of the earliest evidence of pre-colonial occupation in southern Brazil from a geoarchaeological point of view, focusing on stratigraphic and chronological data and the process of formation of archaeological layers. Thirty-three stratigraphic sections were analysed from 31 archaeological sites distributed along the Paraná, Uruguay and Atlantic basins. Evidence of archaeological levels was found in different geomorphological contexts: plateau, slopes, valley bottom, alluvial plains and rockshelters. The results indicate that the oldest archaeological levels in the region were formed in the Late Pleistocene, associated with periods of fluvial incision that signal important changes in the southern river systems, characterized by the formation of alluvial and colluvial-alluvial terraces in the valley bottoms. This is followed in the Lower Holocene by widespread colluvial processes in the incised valleys, alluvium in the middle river courses and anthropogenic deposits in the rockshelters that formed the main ancient levels. In the early Middle Holocene, sedimentary deposits containing archaeological material decrease significantly, marking regional changes in lithic industries. The data indicate that there appears to be a threshold between deposition and archaeology in the Early Holocene, characterized by high stratigraphic resolution, where stratigraphic sequences show greater thickness and density of archaeological levels. Finally, the diversity of inter-regional lithic assemblages is clearly highlighted, marked by the predominance of industries on pebbles and blocks, the debitage of flakes and blades as a support for various tools in the interior basins and the shaping of small projectile points on the Atlantic slope.     

Human cortical bone: the SiNuPrOs model

Many models that have been developed for cortical bone oversimplify much of the architectural and physical complexity. With SiNuPrOs model, a more complete approach is investigated: it is multiscale because it contains five structural levels and multi physic because it takes into account simultaneously structure (with various properties: elasticity, piezoelectricity, porous medium), fluid and mineralization process modelization. The multiscale aspect is modeled by using 18 structural parameters in a specific application of the mathematical theory of homogenization and 10 other physical parameters are necessary for the multi physic aspect. The modelization of collagen as a piezoelectric medium has needed the development of a new behaviour law allowing a better simulation of the effect of a medium considered as evolving during a mineralization process. Then the main interest of SiNuPrOs deals with the possibility to study, at each level of the cortical architecture, either the elastic properties or the fluid motion or the piezoelectric effects or both of them. All these possibilities constitute a very large work and all this mass of information (fluid aspects, even at the nanoscopic scale, piezoelectric phenomena and simulations) will be presented in several papers. This first one is only devoted to the presentation of this model with an application to the computation of elastic properties at the macroscopic scale. The computational methods have been packed into software also called SiNuPrOs and allowing a large number of predictive simulations corresponding to various different configurations.     

The cell pushes back: The Arp2/3 complex is a key orchestrator of cellular responses to environmental forces

The Arp2/3 complex orchestrates the formation of branched actin networks at the interface between the cytoplasm and membranes. Although it is widely appreciated that these networks are useful for scaffolding, creating pushing forces and delineating zones at the membrane interface, it has only recently come to light that branched actin networks are mechanosensitive, giving them special properties. Here, we discuss recent advances in our understanding of how Arp2/3-generated actin networks respond to load forces and thus allow cells to create pushing forces in responsive and tuneable ways to effect cellular processes such as migration, invasion, phagocytosis, adhesion and even nuclear and DNA damage repair.