Simulation of Polymer Solutions by Dissipative Particle Dynamics

Abstract

Dissipative Particle Dynamics (DPD) is employed to model the dynamics and rheology of polymer solutions, and suspensions of spherical particles with adsorbed polymers. Static and dynamic scaling relationships for the variation of radius of gyration and relaxation time with polymer chain length are reviewed, demonstrating that the DPD polymer solution model correctly represents the effects of hydrodynamic interaction and excluded volume. Rheological simulations for both polymer solutions and polymer-sphere suspensions predict Newtonian viscosities at low shear rate followed by shear-thinning behavior as a reduced shear rate of unity is approached. Both the Newtonian viscosity and the extent of shear-thinning are greatly enhanced in the case of good solvents, compared to the viscosity curves for polymers and polymer-spheres structures dissolved in theta solvents and poor solvents.     

Plant cell suspension culture rheology

The results of rheological measurements on 10 different plant cell suspension cultures are presented. Nicotiana tabacum (tobacco) suspension cultures grown in serial batch subculture display high viscosity and power law rheology. This "undesirable" rheology is shown to be a result of elongated cell morphology. The rheology of Papaver somniferum (poppy) cell suspensions is quite different; poppy suspensions behave as Newtonian fluids and have relatively low viscosity (less than 15 cP) at fresh cell densities up to 250 g/L. This flow behavior can be attributed to a lack of elongation in batch-grown poppy cells. A simple correlation for the viscosity as a function of cell density is developed for poppy suspensions up to 300 g fresh weight (FW)/L. It is shown that tobacco cells do not elongate when grown in semicontinuous culture (daily media replacement). These semicontinuously cultured cells have rheological behavior that is indistinguishable from that of poppy, further confirming the dependence of rheology on plant cell morphology. The rheology of a wide variety of other plant suspensions at 200 g FW/L is presented. Most cell suspensions, including soybean, cotton, bindweed, and potato, display low viscosities similar to poppy suspensions. Only carrot and atriplex exhibit slight pseudoplastic behavior which corresponded to a slight degree of cellular elongation for these cultures. This demonstrates that complex rheology associated with elongated cell morphology is much less common than low-viscosity Newtonian behavior. High viscosity in plant cell culture is therefore not an intrinsic characteristic of plant cells but, instead, is a result of the ability to grow cultures to extremely high cell densities due to low biological oxygen demand. (c) 1993 John Wiley & Sons, Inc.     

Effects of cell motility and morphology on the rheology of algae suspensions

Algae have been proposed as a source of biofuels and high value chemical products, but if this potential is to be fully realised, it is crucial to understand the factors affecting the suspension rheology. Suspensions of three algae species, Tetraselmis chuii, Chlorella sp. and Phaeodactylum tricornutum, were sheared in a rotational rheometer in order to characterise their rheology and examine the effects of cell concentration, motility and morphology. The volume fraction ranged from 0.05 to 0.2, and the shear rate from 20 to 200 s^?1. The rheology measurements are fitted to the Herschel-Bulkley model, and the intrinsic viscosity is estimated using both Einstein’s equation and the Krieger-Dougherty model, which are found to perform well for low concentrations. The intrinsic viscosity of T. chuii suspensions is shown not to be constant, but decreases with strain rate, indicating that the suspension viscosity is less sensitive to the cell concentration at high strain rates. The rate of decline is constant for strain rates below approximately 100 s^?1, after which it continues to decline linearly, but at a slower rate. It is speculated that this transition at 100 s^?1 is related to the appearance of flocculation at low strain rates. The effect of the cell motility on the rheology of T. chuii suspensions is investigated by comparing the rheology of motile and passive cells. The shear-thinning behaviour is absent and the effective viscosity is considerably lower for the passive cell suspensions, indicating that the motility of the T. chuii cells causes them to align to resist the flow. In contrast, the Chlorella sp. suspensions exhibit shear-thickening behaviour, which has not previously been reported. Finally, the influence of the effective aspect ratio on the cell suspensions is examined by comparing the intrinsic viscosity of all three species. The algal species with the largest aspect ratio, P. tricornutum, has the largest intrinsic viscosity, while the smallest aspect ratio strain, Chlorella sp., has the smallest viscosity. However, it is shown that the increase in viscosity of motile compared to non-motile T. chuii suspensions cannot be attributed to a change in the effective aspect ratio of individual cells due to the motion of the flagella alone.     

Mesoscopic dynamics of colloids simulated with dissipative particle dynamics and fluid particle model

We report results of numerical simulations of complex fluids, using a combination of discrete-particle methods. Our molecular modeling repertoire comprises three simulation techniques: molecular dynamics (MD), dissipative particle dynamics (DPD), and the fluid particle model (FPM). This type of model can depict multi-resolution molecular structures (see the Figure) found in complex fluids ranging from single micelle, colloidal crystals, large-scale colloidal aggregates up to the mesoscale processes of hydrodynamical instabilities in the bulk of colloidal suspensions. We can simulate different colloidal structures in which the colloidal beds are of comparable size to the solvent particles. This undertaking is accomplished with a two-level discrete particle model consisting of the MD paradigm with a Lennard-Jones (L-J) type potential for defining the colloidal particle system and DPD or FPM for modeling the solvent. We observe the spontaneous emergence of spherical or rod-like micelles and their crystallization in stable hexagonal or worm-like structures, respectively. The ordered arrays obtained by using the particle model are similar to the 2D colloidal crystals observed in laboratory experiments. The micelle shape and its hydrophobic or hydrophilic character depend on the ratio between the scaling factors of the interactions between colloid–colloid to colloid–solvent. Unlike the miscellar arrays, the colloidal aggregates involve the colloid–solvent interactions prescribed by the DPD forces. Different from the assumption of equilibrium growth, the two-level particle model can display much more realistic molecular physics, which allows for the simulation of aggregation for various types of colloids and solvent liquids over a very broad range of conditions. We discuss the potential prospects of combining MD, DPD, and FPM techniques in a single three-level model. Finally, we present results from large-scale simulation of the Rayleigh–Taylor instability and dispersion of colloidal slab in 2D and 3D. Electronic supplementary material to this paper can be obtained by using the Springer LINK server located at http://dx.doi.org/10.1007/s00894-001-0068-3.Electronic Supplementary Material available.     

Jamming and gelation of dense beta-casein micelle suspensions

The rheology of dense suspensions of beta-casein micelles is investigated at pH 6. For a given temperature, the viscosity increases dramatically at a critical concentration (Cc) of about 100 g/L due to jamming of the micelles. For a given concentration close to and above Cc, the viscosity of dense suspensions decreases strongly with increasing temperature because Cc increases. The suspensions show weak shear thickening followed by strong shear thinning. At lower pH, that is, closer to the isoelectric point, spontaneous gelation is observed, which is favored by lowering the temperature and addition of sodium polyphosphate. The gelation process is studied at pH 5.5 by rheology and light scattering.     

Non‐Newtonian rheology in suspension cell cultures significantly impacts bioreactor shear stress quantification

The fields of regenerative medicine and tissue engineering require large‐scale manufacturing of stem cells for both therapy and recombinant protein production, which is often achieved by culturing cells in stirred suspension bioreactors. The rheology of cell suspensions cultured in stirred suspension bioreactors is critical to cell growth and protein production, as elevated exposure to shear stress has been linked to changes in growth kinetics and genetic expression for many common cell types. Currently, little is understood on the rheology of cell suspensions cultured in stirred suspension bioreactors. In this study, we present the impact of three common cell culture parameters, serum content, cell presence, and culture age, on the rheology of a model cell line cultured in stirred suspension bioreactors. The results reveal that cultures containing cells, serum, or combinations thereof are highly shear thinning, whereas conditioned and unconditioned culture medium without serum are both Newtonian. Non‐Newtonian viscosity was modeled using a Sisko model, which provided insight on structural mechanisms driving the rheological behavior of these cell suspensions. A comparison of shear stress estimated by using Newtonian and Sisko relationships demonstrated that assuming Newtonian viscosity underpredicts both mean and maximum shear stress in stirred suspension bioreactors. Non‐Newtonian viscosity models reported maximum shear stresses exceeding those required to induce changes in genetic expression in common cell types, whereas Newtonian models did not. These findings indicate that traditional shear stress quantification of cell or serum suspensions is inadequate and that shear stress quantification methods based on non‐Newtonian viscosity must be developed to accurately quantify shear stress.     

The effect of solution non-ideality on membrane transport in three-dimensional models of the renal concentrating mechanism

Previous models of the renal concentrating mechanism employ ideal approximations of solution thermodynamics for membrane transport calculation. In three-dimensional models of the renal medulla, predicted urine concentrations reach levels where there idealized approximations begin to break down. In this paper we derive equations that govern membrane transport for non-dilute solutions and use these equations in a three-dimensional model of the concentrating mechanism. New numerical methods were employed that are more stable than those employed previously. Compared to ideal solution models, the urea non-ideality tends to increase predicted osmolarities, whereas NaCl non-ideality decreases predictions.     

Micro-macro link in rheology of erythrocyte and vesicle suspensions

We report on the rheology of dilute suspensions of red blood cells (RBC) and vesicles. The viscosity of RBC suspensions reveals a previously unknown signature: it exhibits a pronounced minimum when the viscosity of the ambient medium is close to the value at which the transition from tank-treading to tumbling occurs. This bifurcation is triggered by varying the viscosity of the ambient fluid. It is found that the intrinsic viscosity of the suspension varies by about a factor of 4 in the explored parameter range. Surprisingly, this significant change of the intrinsic viscosity is revealed even at low hematocrit (5%). We suggest that this finding may be used to detect blood flow disorders linked to pathologies that affect RBC shape and mechanical properties. This opens future perspectives on setting up new diagnostic tools, with great efficiency even at very low hematocrit. Investigations are also performed on giant vesicle suspensions, and compared to RBCs.     

Design of Model Apple Cells Suspensions: Rheological Properties and Impact of the Continuous Phase

The objective of this work is twofold: to develop a relevant model system to study plant cells suspensions’ rheology and to evaluate the impact of the continuous phase composition and viscosity on the rheological behaviour of apple cells suspensions. Model suspensions of individual or clustered apple cells were developed. Rheological behaviours of both type of suspensions were observed separately, suspending from 0.145 g/100mL to 3.48 g/100mL of particles in five model media and in the original apple serum. Our results show that model suspensions successfully reproduce the rheological behaviour of apple purees, following three concentration domains. In particular, cell clusters greatly reproduce the behaviour of bimodal apple purees, suggesting that clusters dominate the rheological behaviour of the whole puree. One of our main result is that continuous phase does not affect elastic properties of suspensions in the concentrated domain since they are essentially governed by particle interactions: G’ values are similar whatever the continuous phase. If the continuous phase has the main impact on diluted suspensions’ viscosity, its effect becomes smaller as particle concentration increases. A lubricating effect was observed in the concentrated domain for continuous phases containing polymers. Presence of polymers may help in structuring the network in the intermediate domain.     

Modification of the Use of the Pipette Filler for Reducing the Hazards of Contamination

An adaptation is described which makes the common propipette readily acceptable for repetitive use. The application of pressure from an appropriate gas to permit rapid delivery of fluids and a method by which the propipette may be used comfortably in one hand make this tool amenable to routine use in a practical attempt to reduce the risks of contamination to both the operator and his cultures.     

An incidental case of dihydropyrimidine dehydrogenase deficiency: One case,multiple challenges

Dihydropyrimidine dehydrogenase (DPD) deficiency is an autosomal recessive disorder that shows large phenotypical variability, ranging from no symptoms to intellectual disability, motor retardation, and convulsions. In addition, homozygous and heterozygous mutation carriers can develop severe 5-fluorouracil (5-FU) toxicity. The lack of genotype-phenotype correlation and the possibility of other factors playing a role in the manifestation of the neurological abnormalities, make the management and education of asymptomatic DPD individuals more challenging. We describe a 3-month-old baby who was incidentally found by urine organic acid testing (done as part of positive newborn screen) to have very high level of thymine and uracil, consistent with DPD deficiency. Since the prevalence of asymptomatic DPD deficiency in the general population is fairly significant (1 in 10,000), we emphasize in this case study the importance of developing a guideline in genetic counseling and patient education for this condition as well as other incidental laboratory findings.     

Impact of cell disruption and polymer recycling upon aqueous two-phase processes for protein recovery

A practical study is presented of the influence of cell debris and polymer recycling upon the operation of two-stage acqueous two-phase systems (ATPS) for the recovery of yeast bulk protein, pyruvate kinase and fumarase. Brewers' yeast was disrupted using one of two types of high-pressure homogenisers or a bead mill. The different cell debris suspensions were partitioned in a single PEG-phosphate ATPS extraction and the efficiency of solid-liquid separation was examined. A continuously operated two-stage ATPS process, using spray columns, is presented and practical problems of polymer recycling are discussed. Conclusions are drawn concerning the generic implementation and operational stability of ATPS in practical protein recoveries.     

The oxidation of NN-dimethyl-p-phenylenediamine by oxidizing agents and by caeruloplasmin

1. The oxidation of NN-dimethyl-p-phenylenediamine (DPD) by inorganic oxidants and by caeruloplasmin was studied. Some experiments were also made with NNN'N'-tetramethyl-p-phenylenediamine (TPD). 2. E(mM) (550) of the first free radical oxidation product of DPD (DPD(+)) was 9.8 and E(mM) (563) of the corresponding product of TPD (TPD(+)) was 12.5. 3. The non-enzymic decomposition of DPD(+) was studied with respect to temperature, pH, concentration and DPD/DPD(+) ratio, thus defining conditions for enzyme experiments under which DPD(+) extinction at 550mmu was proportional to enzyme activity. 4. Rates of oxidation of DPD to DPD(+) by caeruloplasmin were constant over a range of DPD concentrations. At low DPD concentrations a lag period occurred, which was eliminated by addition of DPD(+). 5. A lag period was not observed with TPD, but at low TPD concentrations the rate of TPD(+) formation was greater when TPD(+) was added. This suggests that TPD(+) may compete weakly as a substrate with TPD and may be oxidized further by the enzyme before a non-enzymic reaction with TPD to form more TPD(+). 6. With DPD sulphate or acetate or TPD sulphate as substrate, Lineweaver-Burk plots were curved. With DPD hydrochloride the chloride ion caused inhibition at higher concentrations, opposing the curvature. 7. Curved Lineweaver-Burk plots were interpreted in terms of two types of substrate binding site with different K(m) values but similar V(max.) values. 8. The apparent thermodynamic changes associated with enzyme-substrate-complex formation at the sites with higher K(m) suggest that considerable conformational change may occur on binding at these sites. 9. With substrate concentrations at which only the low-K(m) sites are involved 2mol. of DPD(+)/mol. of caeruloplasmin are formed before a steady state is established. At higher substrate concentrations up to 3.2mol. of DPD(+)/mol. of caeruloplasmin are formed at this initial stage. 10. Results are discussed in relation to caeruloplasmin structures in which (a) two valence-changing and two permanently cuprous copper atoms are more accessible than the remaining four copper atoms or (b) binding of substrate at one site hinders access of substrate to another site.     

Critical evaluation of scientific articles and other sources of information: an introduction to evidence-based veterinary medicine

The purpose of this paper is to briefly review key concepts regarding critical reading of the scientific literature to make informed decisions, in the context of evidence-based veterinary medicine. Key concepts are reviewed, based on the broader experience in human medicine, with adaptations, as indicated, to veterinary medicine. That a paper has been published in a peer-reviewed journal does not guarantee its credibility; guidelines are given regarding the general merit of different kinds of articles, as well as checklists and criteria that can be used to assess a paper. Specific study designs, their merits and limitations, are briefly discussed. Standard numerical indices for assessment of studies involving treatments and for assessments of diagnostic tests are summarized. Criteria for assessing drug trials are presented. The principles of statistical analysis are described, including practical considerations and common errors. Finally, numerous sources of bias are reviewed.     

A neonate with recurrent vomiting and generalized hypotonia diagnosed with a deficiency of dihydropyrimidine dehydrogenase

Deficiency of dihydropyrimidine dehydrogenase (DPD) is a rare inborn error of pyrimidine metabolism. To date, only about 50 patients are known worldwide. The clinical picture is varied and is not yet fully described. Most patients are diagnosed at the age of 1-3 years. We present a patient diagnosed 8 weeks postpartum.The female patient presented in the first 3 days after birth with agitation, choking, and vomiting. Six weeks later, the patient presented again with vomiting and insufficient weight gain. Metabolic screening of urine showed a strongly increased excretion of uracil and thymine, with no other abnormalities. This suggested a deficiency of DPD which was confirmed by enzyme analysis in peripheral blood mononucleair (PBM) cells (patient: activity <0.01 nmol/mg/h; controls: 9.9 +/- 2.8 nmol/mg/h). The patient was homozygous for the IVS14+1G>A mutation.MRI of the brain showed some cerebral atrophy; myelinization appeared normal. Many patients with DPD-deficiency suffer from convulsions and mental retardation, some show microcephaly, feeding difficulties, autism, and hypertonia. Our patient showed feeding difficulties and in the second half-year she developed slight motor retardation and generalized hypotonia. Further observation of the development of the patient may shed more light on the relationship between clinical symptoms and DPD deficiency. DPD deficiency may present in newborns with vomiting and hypotonia as the main symptoms.     

The pressure-flow relation in resting rat skeletal muscle perfused with pure erythrocyte suspensions

In spite of numerous investigations of erythrocyte rheology, there is limited information about the influence of erythrocyte suspensions on whole organ pressure-flow relationships. In this study, we present whole organ pressure-flow curves for resting vasodilated gracilis muscle of the rat, in which the microanatomy and vessel properties have been determined previously. For pure erythrocyte suspensions from donor rats, the organ resistance increases only mildly with perfusion time (less than a 5% shift over a one-hour perfusion time), while in contrast, erythrocyte suspensions containing leukocytes show an increases of resistance near 100% over a period of 25 min. Variation in pressure-flow curves in the muscle at the same arterial hematocrit between different rats is less than 15%. The pressure-flow relation for pure erythrocyte suspensions depends on hematocrit. Shear thinning is exhibited at high hematocrits, while Newtonian behavior is approached at arterial hematocrits below 15%. The whole organ apparent viscosity for pure erythrocyte suspensions (normalized by cell-free plasma resistance) is a non-linear function of hematocrit; at physiological pressures, it reaches values comparable to those of apparent viscosities measured in rotational viscometers or in in vitro tube flow (diameters greater than 0.8 mm). The apparent viscosities estimated from the whole organ experiments tend to be higher than those measured in straight tubes under in vitro conditions. The pressure-flow curves for pure erythrocyte suspensions are shifted towards lower pressures than the curves for mixed suspensions of erythrocytes at the same hematocrit and with leukocytes at physiological cell counts. These acute experiments show that pure erythrocyte suspensions yield highly reproducible resistances in the skeletal muscle microcirculation with dilated arterioles. Relative apparent viscosities measured in vivo are higher than those measured in straight glass tubes of comparable dimesions.     

A Neonate with Recurrent Vomiting and Generalized Hypotonia Diagnosed with a Deficiency of Dihydropyrimidine Dehydrogenase

Deficiency of dihydropyrimidine dehydrogenase (DPD) is a rare inborn error of pyrimidine metabolism. To date, only about 50 patients are known worldwide. The clinical picture is varied and is not yet fully described. Most patients are diagnosed at the age of 1–3 years. We present a patient diagnosed 8 weeks postpartum.

The female patient presented in the first 3 days after birth with agitation, choking, and vomiting. Six weeks later, the patient presented again with vomiting and insufficient weight gain. Metabolic screening of urine showed a strongly increased excretion of uracil and thymine, with no other abnormalities. This suggested a deficiency of DPD which was confirmed by enzyme analysis in peripheral blood mononucleair (PBM) cells (patient: activity <0.01 nmol/mg/h; controls: 9.9 ± 2.8 nmol/mg/h). The patient was homozygous for the IVS14+1G>A mutation.

MRI of the brain showed some cerebral atrophy; myelinization appeared normal. Many patients with DPD-deficiency suffer from convulsions and mental retardation, some show microcephaly, feeding difficulties, autism, and hypertonia. Our patient showed feeding difficulties and in the second half-year she developed slight motor retardation and generalized hypotonia. Further observation of the development of the patient may shed more light on the relationship between clinical symptoms and DPD deficiency. DPD deficiency may present in newborns with vomiting and hypotonia as the main symptoms.     

High-performance liquid chromatography method to analyze free and total urinary pyridinoline and deoxypyridinoline

The pyridinium cross-links pyridinoline (PYD) and deoxypyridinoline (DPD) are established markers of bone resorption measured in blood and urine and are used to investigate bone metabolism and manage bone diseases. Unfortunately, the currently observed interlaboratory variability caused by inconsistent assay calibration limits the optimal use of these markers. A high-performance liquid chromatography (HPLC)-based assay was developed using synthetic PYD and DPD as calibrators to analyze free and total PYD and DPD in urine. The spectroscopic characteristics of the synthetic calibrators were identical to those of calibrators isolated from bone. The mean intraassay variabilities of the HPLC method were 4.1 and 3.8%, respectively, for total DPD and PYD and 9.8 and 9.5%, respectively, for free DPD and PYD. The mean interassay variabilities were 9.1 and 8.2% for total DPD and PYD and 8.6 and 7.0% for free DPD and PYD, respectively. The mean recoveries were 98.1% for total DPD, 100.8% for total PYD, 98.6% for free DPD, and 94.9% for free PYD. The method exhibits a good correlation with a commercial immunoassay and with other HPLC assays currently used in hospital laboratories.