Correlation of droplet elasticity and volume fraction effects on emulsion dynamics.

The rheological properties of emulsions are of considerable importance in a diverse range of scenarios. Here we describe a superposition of the effects of droplet elasticity and volume fraction on the dynamics of emulsions. The superposition is governed by physical interactions between droplets, and provides a new mechanism for modifying the flow behavior of emulsions, by controlling the elasticity of the dispersed phase. We investigate the properties of suspensions of emulsified wormlike micelles (WLM). Dense suspensions of the emulsified WLM droplets exhibit thermally responsive properties in which the viscoelastic moduli decrease by an order of magnitude over a temperature range of 0 °C to 25 °C. Surprisingly, the dependence of modulus on volume fraction is independent of droplet stiffness. Instead, the emulsion modulus scales as a power-law with volume fraction with a constant exponent across all temperatures even as the droplet properties change from elastic to viscous. Nevertheless, the underlying droplet dynamics depend strongly on temperature. From stress relaxation experiments, we quantify droplet dynamics across the cage breaking time scale below which the droplets are locally caged by neighbors and above which the droplets escape their cages to fully relax. For elastic droplets and high volume fractions, droplets relax less stress on short time scales and the terminal relaxations are slower than for viscous droplets and lower volume fractions. Characteristic measures of the short and long-time dynamics are highly correlated for variations in both temperature and emulsion concentration, suggesting that thermal and volume fraction effects represent independent parameters to control emulsion properties.

Controlling orientational order in block copolymers using low-intensity magnetic fields.

The interaction of fields with condensed matter during phase transitions produces a rich variety of physical phenomena. Self-assembly of liquid crystalline block copolymers (LC BCPs) in the presence of a magnetic field, for example, can result in highly oriented microstructures due to the LC BCP's anisotropic magnetic susceptibility. We show that such oriented mesophases can be produced using low-intensity fields (<0.5 T) that are accessible using permanent magnets, in contrast to the high fields (>4 T) and superconducting magnets required to date. Low-intensity field alignment is enabled by the addition of labile mesogens that coassemble with the system's nematic and smectic A mesophases. The alignment saturation field strength and alignment kinetics have pronounced dependences on the free mesogen concentration. Highly aligned states with orientation distribution coefficients close to unity were obtained at fields as small as 0.2 T. This remarkable field response originates in an enhancement of alignment kinetics due to a reduction in viscosity, and increased magnetostatic energy due to increases in grain size, in the presence of labile mesogens. These developments provide routes for controlling structural order in BCPs, including the possibility of producing nontrivial textures and patterns of alignment by locally screening fields using magnetic nanoparticles.

Dynamics of a thermo-responsive microgel colloid near to the glass transition.

In a previous study, we used diffusing wave spectroscopy (DWS) to investigate the aging signatures of a thermo-sensitive colloidal glass and compared them with those of molecular glasses from the perspective of the Kovacs temperature-jump, volume recovery experiments [X. Di, K. Z. Win, G. B. McKenna, T. Narita, F. Lequeux, S. R. Pullela, and Z. Cheng, Phys. Rev. Lett. 106, 095701 (2011)]. In order to further look into the glassy behavior of colloidal systems, we have synthesized a new core/shell particle with lower temperature sensitivity and studied the aging signatures of concentrated systems, again following Kovacs' protocol. Similar signatures of aging to those observed previously were seen in this new system. Moreover, a systematic study of the temperature dependence of the dynamics of the new system for different weight concentrations was performed and the dynamic fragility index m was determined. We have also explored the use of the properties determined from the DWS measurements to obtain macroscopic rheological parameters - storage modulus G(')(ω) and loss modulus G(″)(ω) - using a generalized Stokes-Einstein approach. The micro-rheological and macro-rheological values are in reasonable agreement.

Evaluation of heterogeneity measures and their relation to the glass transition.

For most phase transitions, dynamic slowdown is accompanied by a static structure change. However, in the case of the supercooled liquid, which is a special liquid state below the melting temperature, one observes pronounced dynamic slowdown, i.e., diffusion coefficient, relaxation time, and viscosity change 10-14 orders of magnitude within a relatively small temperature range. This occurs without the pronounced static structure change observed in other phase transitions. Over the past several decades, there has been extensive research aimed to understand why the glass transition occurs, to establish what the glass transition exactly is, and to improve our understanding of how molecules move near to the glass transition. In the present work, we have examined the idea that the dramatic reduction in molecular mobility or dynamic slowdown in a supercooled liquid during cooling from above T(g) occurs because of the increasing length scale of heterogeneous subregions, or the cooperatively rearranging regions (CRR) proposed by Adam and Gibbs. Although there is little doubt about the existence of microscopic heterogeneous regions, the absence of the "universal" parameters to characterize the temperature dependent heterogeneity data and type of temperature divergence among different parameters over the same temperature range suggests the possibility that the heterogeneity itself may not relate to the CRR directly and thus may not be the key cause of the glass transition phenomenon. It remains an important research challenge to identify which, if any, of the heterogeneity parameters relates in a causal manner to the glass transition.

Gelation via ion exchange in discotic suspensions.

The phase behavior of charged disk suspensions displays a strong dependence on ionic strengths, as the interplay between excluded volume and electrostatic interactions determines the formation of glasses, gels, and liquid crystal states. The various ions in natural soil or brine, however, could present additional effects, especially considering that most platelet structures bear a momentous ion-exchange capacity. Here we observed how ion exchange modulates and controls the interaction between individual disks and leads to unconventional phase transitions from isotropic gel to nematic gel and finally to nematic liquid crystals.

Signatures of structural recovery in colloidal glasses.

Colloids near the glass concentration are often taken as models for molecular glasses. Yet, an important aspect of the dynamics of molecular glasses, structural recovery, has not been elucidated in colloids. We take advantage of a thermosensitive colloidal suspension to study the structural recovery after concentration jumps by using diffusing wave spectroscopy. The three classical aging signatures observed in molecular glasses are studied and the results are compared with those typical of molecular glasses. For the intrinsic isotherms, unlike molecular glasses, the colloid shows huge changes in relaxation time at equilibrium while the times required to reach the equilibrium state are nearly constant. For asymmetry of approach, we find a similar nonlinearity to that observed in the molecular glasses. For the memory experiment, while a memory effect is seen, the response is qualitatively different from that in molecular glasses.

CARAT: a novel method for allelic detection of DNA copy number changes using high density oligonucleotide arrays.

BACKGROUND: DNA copy number alterations are one of the main characteristics of the cancer cell karyotype and can contribute to the complex phenotype of these cells. These alterations can lead to gains in cellular oncogenes as well as losses in tumor suppressor genes and can span small intervals as well as involve entire chromosomes. The ability to accurately detect these changes is central to understanding how they impact the biology of the cell. RESULTS: We describe a novel algorithm called CARAT (Copy Number Analysis with Regression And Tree) that uses probe intensity information to infer copy number in an allele-specific manner from high density DNA oligonuceotide arrays designed to genotype over 100,000 SNPs. Total and allele-specific copy number estimations using CARAT are independently evaluated for a subset of SNPs using quantitative PCR and allelic TaqMan reactions with several human breast cancer cell lines. The sensitivity and specificity of the algorithm are characterized using DNA samples containing differing numbers of X chromosomes as well as a test set of normal individuals. Results from the algorithm show a high degree of agreement with results from independent verification methods. CONCLUSION: Overall, CARAT automatically detects regions with copy number variations and assigns a significance score to each alteration as well as generating allele-specific output. When coupled with SNP genotype calls from the same array, CARAT provides additional detail into the structure of genome wide alterations that can contribute to allelic imbalance.

Dynamic model based algorithms for screening and genotyping over 100 K SNPs on oligonucleotide microarrays.

MOTIVATION: A high density of single nucleotide polymorphism (SNP) coverage on the genome is desirable and often an essential requirement for population genetics studies. Region-specific or chromosome-specific linkage studies also benefit from the availability of as many high quality SNPs as possible. The availability of millions of SNPs from both Perlegen and the public domain and the development of an efficient microarray-based assay for genotyping SNPs has brought up some interesting analytical challenges. Effective methods for the selection of optimal subsets of SNPs spanning the genome and methods for accurately calling genotypes from probe hybridization patterns have enabled the development of a new microarray-based system for robustly genotyping over 100,000 SNPs per sample. RESULTS: We introduce a new dynamic model-based algorithm (DM) for screening over 3 million SNPs and genotyping over 100,000 SNPs. The model is based on four possible underlying states: Null, A, AB and B for each probe quartet. We calculate a probe-level log likelihood for each model and then select between the four competing models with an SNP-level statistical aggregation across multiple probe quartets to provide a high-quality genotype call along with a quality measure of the call. We assess performance with HapMap reference genotypes, informative Mendelian inheritance relationship in families, and consistency between DM and another genotype classification method. At a call rate of 95.91% the concordance with reference genotypes from the HapMap Project is 99.81% based on over 1.5 million genotypes, the Mendelian error rate is 0.018% based on 10 trios, and the consistency between DM and MPAM is 99.90% at a comparable rate of 97.18%. We also develop methods for SNP selection and optimal probe selection. AVAILABILITY: The DM algorithm is available in Affymetrix's Genotyping Tools software package and in Affymetrix's GDAS software package. See http://www.affymetrix.com for further information. 10 K and 100 K mapping array data are available on the Affymetrix website.

Alternative base calling method for resequencing microarrays.

Analysis of high density oligonucleotide arrays for resequencing requires methods which are highly robust and accurate. We introduce an alternative base calling method built upon ABACUS with the particular advantage of achieving a very low rate for false positive detection of heterozygotes.

MARA: a novel approach for highly multiplexed locus-specific SNP genotyping using high-density DNA oligonucleotide arrays.

We have developed a locus-specific DNA target preparation method for highly multiplexed single nucleotide polymorphism (SNP) genotyping called MARA (Multiplexed Anchored Runoff Amplification). The approach uses a single primer per SNP in conjunction with restriction enzyme digested, adapter-ligated human genomic DNA. Each primer is composed of common sequence at the 5' end followed by locus-specific sequence at the 3' end. Following a primary reaction in which locus-specific products are generated, a secondary universal amplification is carried out using a generic primer pair corresponding to the oligonucleotide and genomic DNA adapter sequences. Allele discrimination is achieved by hybridization to high-density DNA oligonucleotide arrays. Initial multiplex reactions containing either 250 primers or 750 primers across nine DNA samples demonstrated an average sample call rate of approximately 95% for 250- and 750-plex MARA. We have also evaluated >1000- and 4000-primer plex MARA to genotype SNPs from human chromosome 21. We have identified a subset of SNPs corresponding to a primer conversion rate of approximately 75%, which show an average call rate over 95% and concordance >99% across seven DNA samples. Thus, MARA may potentially improve the throughput of SNP genotyping when coupled with allele discrimination on high-density arrays by allowing levels of multiplexing during target generation that far exceed the capacity of traditional multiplex PCR.

Parallel genotyping of over 10,000 SNPs using a one-primer assay on a high-density oligonucleotide array.

The analysis of single nucleotide polymorphisms (SNPs) is increasingly utilized to investigate the genetic causes of complex human diseases. Here we present a high-throughput genotyping platform that uses a one-primer assay to genotype over 10,000 SNPs per individual on a single oligonucleotide array. This approach uses restriction digestion to fractionate the genome, followed by amplification of a specific fractionated subset of the genome. The resulting reduction in genome complexity enables allele-specific hybridization to the array. The selection of SNPs was primarily determined by computer-predicted lengths of restriction fragments containing the SNPs, and was further driven by strict empirical measurements of accuracy, reproducibility, and average call rate, which we estimate to be >99.5%, >99.9%, and>95%, respectively [corrected]. With average heterozygosity of 0.38 and genome scan resolution of 0.31 cM, the SNP array is a viable alternative to panels of microsatellites (STRs). As a demonstration of the utility of the genotyping platform in whole-genome scans, we have replicated and refined a linkage region on chromosome 2p for chronic mucocutaneous candidiasis and thyroid disease, previously identified using a panel of microsatellite (STR) markers.

Genotyping over 100,000 SNPs on a pair of oligonucleotide arrays.

We present a genotyping method for simultaneously scoring 116,204 SNPs using oligonucleotide arrays. At call rates >99%, reproducibility is >99.97% and accuracy, as measured by inheritance in trios and concordance with the HapMap Project, is >99.7%. Average intermarker distance is 23.6 kb, and 92% of the genome is within 100 kb of a SNP marker. Average heterozygosity is 0.30, with 105,511 SNPs having minor allele frequencies >5%.

Algorithms for large-scale genotyping microarrays.

MOTIVATION: Analysis of many thousands of single nucleotide polymorphisms (SNPs) across whole genome is crucial to efficiently map disease genes and understanding susceptibility to diseases, drug efficacy and side effects for different populations and individuals. High density oligonucleotide microarrays provide the possibility for such analysis with reasonable cost. Such analysis requires accurate, reliable methods for feature extraction, classification, statistical modeling and filtering. RESULTS: We propose the modified partitioning around medoids as a classification method for relative allele signals. We use the average silhouette width, separation and other quantities as quality measures for genotyping classification. We form robust statistical models based on the classification results and use these models to make genotype calls and calculate quality measures of calls. We apply our algorithms to several different genotyping microarrays. We use reference types, informative Mendelian relationship in families, and leave-one-out cross validation to verify our results. The concordance rates with the single base extension reference types are 99.36% for the SNPs on autosomes and 99.64% for the SNPs on sex chromosomes. The concordance of the leave-one-out test is over 99.5% and is 99.9% higher for AA, AB and BB cells. We also provide a method to determine the gender of a sample based on the heterozygous call rate of SNPs on the X chromosome. See http://www.affymetrix.com for further information. The microarray data will also be available from the Affymetrix web site. AVAILABILITY: The algorithms will be available commercially in the Affymetrix software package.

Large-scale genotyping of complex DNA.

Genetic studies aimed at understanding the molecular basis of complex human phenotypes require the genotyping of many thousands of single-nucleotide polymorphisms (SNPs) across large numbers of individuals. Public efforts have so far identified over two million common human SNPs; however, the scoring of these SNPs is labor-intensive and requires a substantial amount of automation. Here we describe a simple but effective approach, termed whole-genome sampling analysis (WGSA), for genotyping thousands of SNPs simultaneously in a complex DNA sample without locus-specific primers or automation. Our method amplifies highly reproducible fractions of the genome across multiple DNA samples and calls genotypes at >99% accuracy. We rapidly genotyped 14,548 SNPs in three different human populations and identified a subset of them with significant allele frequency differences between groups. We also determined the ancestral allele for 8,386 SNPs by genotyping chimpanzee and gorilla DNA. WGSA is highly scaleable and enables the creation of ultrahigh density SNP maps for use in genetic studies.