New England Complex Fluids Workgroup

Abstracts for Invited Talks and Sound Bites:

Invited Talks

1. Invited Speaker; Julio M. Fernandez

Columbia University

"The folding and chemistry of single proteins under force"
We aim to understand how mechanical forces, over the full biological spectrum, affect the dynamics and chemistry of proteins. Using molecular biology techniques, we engineered tandem modular proteins that are made of identical repeats of a protein of interest. These polyproteins act as handles for atomic force microscopes, without the need for linkers or special attachment chemistry. When such polyproteins are extended by an AFM, their force properties are unique mechanical fingerprints that unambiguously distinguish them from the more frequent non-specific events that plague single molecule studies. Our initial experiments were done by extending polyproteins at constant velocity, resulting in the now familiar sawtooth pattern traces of unfolding. However, in these early experiments, the variables of force, length and loading rate changed simultaneously over wide ranges, and thus yielded only qualitative results. We solved these problems by introducing force-clamp AFM. With this approach, the length of an extending polyprotein is measured while the pulling force is actively kept constant by negative feedback control. Akin to the use of voltage-clamp techniques to study ion channels, the force-clamp technique combined with polyprotein engineering has become a powerful approach to study proteins. We have investigated the force-dependency of protein folding, unfolding and of chemical reactions. From the force-dependence, we extract features of the transition state of these reactions that reveal underlying molecular mechanisms. For example, we found that the distance to the transition state of protein unfolding follows the size of the solvent molecules, implicating them in the transition state structure. Using force pulses, we drove a single protein to a highly extended state, and then upon quenching the force observed how the protein folded (1). Observing a folding reaction over regions hitherto unexplored, uncovered a rich diversity of trajectories of protein folding that had been hidden in bulk experiments. The observations support statistical theories of folding that predicted the absence of defined states and preferred pathways. Perhaps the most striking use of force-clamp spectroscopy so far has been in the study of the effect of force on a chemical reaction. While mortars and pestles have been used for thousands of years to catalyze chemical reactions, it had never been possible to examine a molecule undergoing a chemical reaction while placed under a calibrated and vectorially defined force. We applied a constant stretching force to engineered disulfide bonds and measured their rate of reduction by small molecules and enzymes. These experiments captured the effect of a mechanical force on the rotation and elongation of the disulfide bond as it reached the transition state within the active site of the thioredoxin enzyme (2). More recently, we have observed that these sub-Angstrom scale rearrangements, where enzymatic chemistry takes place, are sensitive to the evolutionary origins of the thioredoxin enzyme (3). Thus, force-clamp AFM, with its remarkable ability to manipulate short recombinant proteins, has become a useful probe of protein dynamics, allowing us to sense conformational changes down to the sub-Angstrom scale (4). Our data will help guide the development of new theories on areas such as enzyme catalysis, the statistical dynamics of a folding polymer and ab initio studies of a chemical reaction while placed under a stretching force; of common occurrence in nature.
Fernandez, J.M. and Li, H. B. Force-clamp spectroscopy monitors the folding trajectory of a single protein (2004), Science, 303: 1674-1678

Wiita et al, (2007) Probing the chemistry of thioredoxin catalysis with force. Nature, 450:124-7.

Perez-Jimenez, et al, (2009). Diversity of Chemical Mechanisms in Thioredoxin Catalysis Revealed by Single-Molecule Force Spectroscopy. Nature Struct. Molec. Biol. 16(8):890-6.

Garcia-Manyes, et al, (2009). Force activated reactivity switch in a bimolecular chemical reaction. Nature Chemistry, 1, 236 - 242.

Keywords:

2. Michael Brenner

Harvard University

"Scaling and shear transformations capture beak shape variation in Darwina~@~Ys Finches"
Evolution by natural selection has resulted in a remarkable diversity of organism morphologies that has long fascinated scientists and served to establish the first relations among species. Despite the essential role of morphology as a phenotype of species, there is not yet a formal, mathematical scheme to quantify morphological phenotype and relate it to both the genotype and the underlying developmental genetics. In this talk, I will discuss our recent work (joint with O. Campas, R. Mallarino, A. Herrell and A. Abzhanov) that demonstrates that the morphological diversity in the beaks of Darwina~@~Ys Finches is quantitatively accounted for by the mathematical group of affine transformations. Specifically, we show that all beak shapes of Ground Finches (genus Geospiza) are related by scaling transformations (a subgroup of the affine group), and the same relationship holds true for all the beak shapes of Tree, Cocos, and Warbler Finches (three distinct genera). This analysis shows that the beak shapes within each of these groups differ only by their scales, such as length and depth, which are genetically controlled by Bmp4 and Calmodulin. By measuring Bmp4 expression in the beak primordia of the species in the genus Geospiza, we provide a quantitative map between beak morphology and the expression levels of Bmp4. The complete morphological variation within the beaks of Darwina~@~Ys finches can be explained by extending the scaling transformations to the entire affine group, by including shear transformations. Altogether our results suggest that the mathematical theory of groups can help decode morphological variation, and points to a potentially hierarchical structure of morphological diversity and the underlying developmental processes.
Keywords:

3. Michael Choma

Yale University

"Microfluidic cardiovascular systems - lessons learned from the fruit fly"

Flow is a defining feature of cardiovascular systems. While the study of hemodynamics in large cardiovascular systems is a maturing field, the study of microfluidic-scale hearts has been gaining momentum over the past decade. Biological flow driven by microfluidic-scale pumps is of interest in both evolutionary biology as well as in clinical medicine. From a biological perspective, microfluidic-scale hearts were an important evolutionary innovation that overcame the decreasing efficiency of diffusion-mediated transport as organism size approached ~1 millimeter. From a medical perspective, not only do early embryonic hearts function in the microfluidic regime, but alterations in hemodynamic forces during early development can have deleterious effects on cardiovascular development.

The fruit fly Drosophila melanogaster is a widely-studied organism in biology and also is an important animal model of human disease. We have used high-speed optical imaging to investigate microfluidic-scale cardiovascular function in this canonical organism. Our work demonstrates that the larval fruit fly heart is an efficient microfluidic pump that drives flow-limited mass transport. Using several measures of cardiovascular performance, we argue that a physiologic homology exists between the open D. melanogaster cardiovascular system and that of closed vertebrate systems. We explore intracardiac as well as extracellular-extravascular microfluidic flow patterns. Finally, we present a comprehensive experimental approach for characterizing microfluidic phenomenon in the fruit fly cardiovascular system, an approach that draws insights from clinical medicine and that focuses on exploring the scientific interface between biology and fluidics.

Keywords:

4. Patrick Underhill

Rensselaer Polytechnic Institute

"Examining the coil-stretch transition in flexible polymers"
The behavior of polymer solutions in elongational flow is important in many applications. An especially important property is the dramatic strain rate hardening resulting from the coil-stretch transition. Predictions of the coil-stretch transition and hysteresis made by DeGennes, Hinch, and others have been verified by visualizing single molecules of double-stranded DNA (ds-DNA). The same behavior has not yet been directly observed in single molecule studies of synthetic polymers or more flexible biopolymers such as single-stranded DNA. Current theories of flexible polymers predict these other polymers will behave in a similar way to ds-DNA. However, my group has very recently predicted that these other polymers could have dramatically different behavior; the coil-stretch transition can be eliminated under some conditions. I will discuss these predictions and how they could impact a wide range of applications.
Keywords:

5. Surita Bhatia

Dept. of Chemical Engineering, UMass-Amherst

"Microstructural Characterization of Glasses and Gels"
There has been a great deal of excitement in recent literature surrounding the behavior of attractive glasses. The well-known repulsive glass can be characterized by one length scale (the hard core diameter). By contrast, in the attractive glass, there is a second characteristic length scale present (the range of the attractive well), and results from mode coupling theory suggest that clusters of particles may form and act to hinder particle motion. Does this translate into a measureable difference in the microstructure of attractive glasses versus other disordered states? In this talk, I will describe our group efforts to answer this question experimentally using ultra-small angle scattering techniques. We have examined a series of model and not-so-model systems, including micelles that behave as adhesive hard spheres, charged soft spheres, charged discs, and neutral discs with bridging polymers. Our work suggests that clustering in attractive glasses leads to Porod-like scattering in attractive glasses at low values of the scattering vector q.
Keywords:

Sound Bites

1. Cabanas

Brandeis University

"Dynamics of Rods and Spheres"
We present here the matter of diffusion in mixtures of rods and spheres. At certain concentrations, mixtures of colloidal rods (fd-virus) and polystyrene spheres which act as hard particles, form lamellar phases. There are many studies on phase behavior of this type of systems, but few dynamic studies of them. Even if our data are not conclusive, we will outline the problem we are dealing with and our future directions.
Keywords: liquid crystals, virus, spheres, dynamics, lamellar, diffusion.

2. Carl Schreck; Jin-Gyu Park, Eric Dufresne, SS Ashwin, Corey O'Hern

Yale University

"Simulation and Analytic Studies on Packings of Anisotropic Objects in a Confined Space"
We study packings of dumbbell-shaped objects in confined spaces. Packings created in a slit of infinite width but limited height exhibit a number of interesting phases for heights between 1 and 2.5 particle diameters. At heights above 2.5 particle diameters, packings become increasingly amorphous. We are examining these packings with analytic methods for calculating configurational entropy (Ashwin and Bowles, Phys. Rev. Lett. 102, 235702 (2009)), and are working closely with experiments on layering effects in colloidal systems of dumbbells.
Keywords: Jamming, Colloids, Shape Anisotropy

3. Dipti

UML

"Smectic A to Nematic Phase Transition of the Aligned Octylcyanobiphenyl Could Bring Faster Response in Smectic Liquid Crystal Devices"
In the smectic liquid crystal devices, more attention has been paying to get smectic phase transition earlier with higher quality. The laser beam steering and the optical shutter applications have also been showing their interest on how fast the smectic phase transition can be reached. Therefore, here we report the energy dynamics of the molecular motion and rearrangement of the octylcyanobiphenly (8CB) liquid crystal molecules at the smectic A to nematic (SmA-N) phase transition in the presence of magnetic field alignment as a function of time, temperature and energy activation. The results indicate that the presence of the alignment in 8CB brings faster response time and an increased energy dynamics with higher activation for the SmA-N phase transition and make the results useful in the smectic liquid crystal devices.
Keywords: Liquid Crystal, Smectic A to Nematic Phase Transition, LCDs

4. Forster

Yale University

"Biomimetic isotropic nanostructures for structural coloration"

Keywords:

5. German; E. Pashkovski, E.R. Dufresne

Yale University

"Imaging stress in skin"

Keywords: Stratum corneum, drying, traction force microscopy,heterogeneous

6. Jin Gyu Park; Jin-Gyu Park, Eric R. Dufresne

Yale University

"Self-assembly of nano-dumbbells into 3D photonic crystals"

Keywords: non-spherical particles, self-assembly, photonic crystals

7. Kang; Brannon.R. McCullough, Matthew Akamatsu, Enrique M. De La Cruz

Yale University

"The role of ion binding in F-actin assembly"
An understanding of ion effects on biopolymer assembly is crucial to clarify the mechanics and thermodynamics of polymerization process at a molecular level. We have examined the role of certain cations (K+ and Mg2+) on actin filament assembly and flexibility by measuring the critical concentration and persistence length. The numbers of potassium and magnesium ions that associate with actin differ during polymerization. We also show an effect of potassium ions on the filament flexibility.
Keywords: Cation binding, F-actin assembly, filament flexibility

8. Lin Shao; Jodie L. Lutkenhaus

Yale University

"Thermal properties of free-standing electrostatic layer-by-layer assemblies"
Layer-by-layer (LbL) assemblies are promising for global energy and health applications, but their materials properties are not well understood. Particularly, little is known about the thermal properties of LbL assemblies because the supporting substrate impedes characterization. It is not initially clear if electrostatic LbL assemblies possess a glass transition temperature or if they are rubbery or glassy. Here, we isolate large areas of poly(allylamine hydrochloride)/poly(acrylic acid) (PAH/PAA) LbL assemblies from low surface energy substrates, which facilitates direct thermal characterization via modulated differential scanning calorimetry (MDSC) and thermal gravimetric analysis (TGA). Surprisingly, a glass transition temperature was not observed for the LbL film even though homopolymer constituents have well-defined glass transitions. Instead, two endothermic events indicated water loss and covalent cross-linking within the LbL assemblies. TGA and Fourier transform infrared (FTIR) spectroscopy confirm the presence of cross-linking reactions. Results highlight that PAH/PAA LbL films are glassy at room temperature, and have low mobility because of the high density of ion pair crosslinks. The techniques presented here are general, and can be applied to any LbL film.
Keywords: Layer-by-layer assemblies, modulated differential scanning calorimetry, polyelectrolyte, poly(acrylic acid), poly(allylamine hydrochloride), thermal properties

9. Lu Zhang

"Dielectrophoresis of Janus Particles in AC Electric Fields"
We examine Janus particles as a model system to understand dielectrophoresis (DEP) of anisotropic colloids and investigate factors governing the DEP response and resultant assembly of anisotropic colloids, such as surface chemistry, inner structures, particle size, medium conductivity and applied frequency. We dis-symmetrize precursor polystyrene particles by creating multi-layered structures via gold-coating and self-assembly of thiol monolayer on one hemisphere, which yields DEP behaviors in sharp contrast to that of homogeneous polystyrene particles: (1) Janus particles with gold-coated hemisphere and Janus particles with assembled COOH-end thiol monolayer on gold-capped hemisphere experience positive DEP; (2) Janus particles with assembled CH3-end thiol monolayer on gold-capped hemisphere exhibit negative DEP to positive DEP crossover frequencies at high medium conductivities, which originates from the dominance of interfacial polarization of the double layer and conductive gold layer at different frequency regimes.
Keywords:

10. Majewski; Manesh Gopinadhan, Woo Sik-Jang, Jodie Lutkenhaus, Chinedum Osuji,

Yale University

"Magnetically aligned lithium-conducting polymer membranes"
We present a novel method of alignment of Li ion-conducting block copolymer with the use of magnetic field. In the studied material the hexagonally closed-packed PEO domains are embedded in non-conducting liquid crystalline matrix responsive to the field. Our technique allows us to control the orientation of PEO channels across the sample. The electrical conductivity of the samples with PEO domains aligned along the conduction direction is an order of magnitude grater than the one for the random domains' orientation.
Keywords: magnetic alignment, liquid crystalline polymers, lithium conducting membranes

11. Melik Demirel

Pennsylvania State University

"Directional Properties of Polymeric Nanofilms"
We introduced a bottom-up process based on vapor phase polymerization as a simple and robust method for fabricating stimuli responsive polymeric nanofilms. The strength of our approach is the ability to study the surface chemistry and film morphology at the same time to control the physicochemical properties of the resulting nanofilms. We will describe our process for creating anisotropic nanofilms and present results concerning the directional wettability and directional folding of nanofilms.
Keywords:

12. Meng; Menachem Elimelech

Yale University

"Aggregation of Fullerene Nanoparticles in Aquesous Phase"
The salt-induced aggregation of fullerene nanoparticles in aqueous phase is monitored by multi-angle static and dynamic light scattering technique. Our results show that the aggregation is diffusion limited when NaCl concentration is above critical coagulation concentration, whereas reaction limited below critical coagulation concentration.
Keywords: Aggregation, Fullerene Nanoparticles, Fractal Dimension

13. Merrill; Hui Cao and Eric R. Dufresne

Yale University

"Random lasing as a probe of soft matter systems"

Keywords: Random Laser

14. Negi; Chinedum Osuji

Yale University

"Stress activated dynamics during structural arrest"
We employ parallel superposition rheology to study the dynamics of an aging colloidal glass in the presence of a mean field stress $\sigma_m$. Over a range of intermediate stresses, the loss modulus exceeds the storage modulus at short times but develops a maximum concomitant with a crossover between the two as the system ages. This is attended by a narrowing of the loss peak on increasing stress. We show that this feature is characteristic of the structural arrest in these materials, which is made observable on reasonable timescales by the activating influence of the stress. The arrest time displays an exponential dependence on inverse stress. These results provide experimental validation of the role of stress as an effective temperature in soft glassy systems as has been advanced in recent theoretical frameworks.
Keywords:

15. Noh;

Yale University

"How non-iridescent colors are generated by quasi-ordered structures of bird feathers"

Keywords:

16. Robert Hoy; Corey S. O'Hern

Yale University

"Minimal Energy Polymer Packings"
We examine the minimal energy packings of tangent sticky hard sphere chains, a toy model for the study of polymer collapse. The covalent bond constraints lead to significant differences from the "colloidal" case.
Keywords:

17. S. S; erzy Blawzdziewicz, Corey O'Hern, Mark Shattuck

Department of Physics and Mechanical Engineering, Yale University New Haven/Benjamin Levich Institute, CCNY, New York

"Effect of Thermalization in Jamming Protocols"
The density at which granular materials, colloids, and other particulate materials jam depends strongly on the protocol. Protocols for generating jammed states have two important components (1) the rate at which the packing fraction is increased and (2) the degree of phase space exploration or thermalization. The latter has been largely ignored in the jamming literature. We describe our studies to investigate how thermalization affects the distribution of jammed states. In the absence of thermalization, the probability distribution of jammed states is proportional to the basin volume distribution for jammed states in the energy or density landscape. We show that thermalization casues large deviations between the probability of jammed states and basin volume distribution, and quantify this effect as a function of system size and degree of thermalization.
Keywords: Jamming, Granular

18. S. S; Jerzy Blawzdziewicz, Corey O'Hern, Mark Shattuck

Department of Physics and Mechanical Engineering, Yale University New Haven/Benjamin Levich Institute, CCNY, New York

"Effect of Thermalization in Jamming Protocols"
The density at which granular materials, colloids, and other particulate materials jam depends strongly on the protocol. Protocols for generating jammed states have two important components (1) the rate at which the packing fraction is increased and (2) the degree of phase space exploration or thermalization. The latter has been largely ignored in the jamming literature. We describe our studies to investigate how thermalization affects the distribution of jammed states. In the absence of thermalization, the probability distribution of jammed states is proportional to the basin volume distribution for jammed states in the energy or density landscape. We show that thermalization casues large deviations between the probability of jammed states and basin volume distribution, and quantify this effect as a function of system size and degree of thermalization.
Keywords: Jamming, Granular

19. Sammalkorpi; Paul R. Van Tassel

Yale University

"Polyelectrolyte adsorption at a conducting surface"
Polyelectrolyte interactions with charged surfaces play a key role in a number of industrial applications, such as selective filtering or separation membranes and sensor substrates, and electrochemical components, such as solid electrolytes in batteries and fuel cells. Typically, polyelectrolyte adsorption is controlled by solution variables such as salt concentration and pH, is spontaneous, and saturates due to interfacial charge build-up (often to the overcompensation). As a result, polyelectrolyte films are usually grown in oppositely charged layers as a stepwise process. In recent experiments, we have uncovered conditions where polyelectrolyte adsorption to a conducting surface may become continuous in the sense of scaling linearly with time over hours. This discovery of continuous layer growth offers an enticing possibility of nanoscale thin film growth in a single step process, but also retains a question of the underlying mechanisms. Here we present a molecular simulation study aimed at understanding mechanistically the continuous adsorption process.
Keywords: polyelectrolyte adsorption, molecular modeling

20. Sujit Datta; Rodrigo Guerra, Kosta Ladavac, Anderson Shum, David A. Weitz

Department of Physics and SEAS, Harvard University

"Mechanics of Particle-Stabilized Emulsions"
Particle-stabilized emulsions come up in a variety of applications, yet their mechanical properties are poorly understood. I will describe our recent experiments studying the bulk mechanics of jammed particle-stabilized emulsions as well as exploring and tuning structure and mechanics at the individual droplet level.
Keywords:

21. Tianqi Shen; Corey S. O'Hern

Yale University

"Coarse Grained Modelling of Protein Gels"
We simulate a solution consisting of Tetratrico Peptide Repeat(TPR) proteins and peptide ligands, which are modeled into polymers and monomers with short range attractive interaction. We are studying gelation behavior under different temperatures, volume fractions and compositions to provide a reference for our collaborators in biology who want to make protein gels in their experiment.
Keywords:

22. Tom Kodger; Joris Sprakel, Rodrigo Guerra, David A. Weitz

SEAS, Harvard University

"Aqueous Hard Sphere Colloids"
While several hard sphere colloidal systems exist, each has its own limitations. We have recently developed a new density and index matched hard sphere colloidal system that employs a binary mixture of non-volatile solvents. I will provide an overview of the synthesis procedure and highlight the flexibility and benefits of the new system for experimental colloidal physics.
Keywords: colloid, hard sphere, ATRP

23. Vinodkumar Saranathan; Richard O. Prum

Department of Ecology and Evolutionary Biology, Peabody Museum of Natural History, and Center for Research on Interface Structures sand Phenomena (CRISP), Yale University, New Haven, CT 06520

"Structure and Optical Function of Avian Amorphous Photonic Nanostructures in Feather Barbs"
Non-iridescent feather structural colours constitute a conspicuous aspect of the avian phenotype and frequently used in social and sexual signalling. They are produced by coherent scattering of visible light by 3D self-assembled, quasi-ordered or amorphous nanostructures of β-keratin and air in the medullary cells of feather barbs. Despite their intriguing isotropic optical properties and the burgeoning interest on their signal content, the mechanistic basis of colour production by such amorphous photonic nanostructures remains uncertain, perhaps because current electron microscopy based Fourier methods are inadequate. Using small angle x-ray scattering (SAXS), we quantitatively assay multiple, distinct structurally coloured plumage patches from 162 species belonging to 41 avian families, in order to robustly characterise these nanostructures for the first time. Based on the SAXS structural information, we accurately distinguish between the two classes of feather barb nanostructures: spheres and channels. We apply single scattering theory to predict the optical function of the nanostructures directly from the SAXS structural data and compare it with spectrophotometric measurements. In general, the sphere-type nanostructures seem to optically outperform the channels in terms of the spectral purity or saturation of the hue. We also describe the ubiquitous phenomenon of double scattering from many nanostructures that gives rise to a second-order reflection typically in the UV in addition to the primary reflection peak, and distinct from Mie resonance, the recognition of which may be relevant to behavioural studies, given that birds can see in the UV and the ubiquity of UV reflection in the avian plumage.
Keywords: bio-photonics, structural color, self-assembly, phase separation

24. Woo-Sik Jang; Jodie L. Lutkenhaus

Post-Doctoral Associate

"Thermal behaviors of poly(allylamine hydrochloride)/poly(acrylic acid) ultra thin layer-by-layer assembly"
Polymeric nanoscale structure, like ultra thin film and nanotubes, is increasingly important in biomedical applications, mobile power solutions, and display industry. The nanoscale structure of polymers behaves strikingly different from the bulk structure due to confinement effects. We report the confinement effects of poly(allylamine hydrochloride) (PAH) and poly(acrylic acid) (PAA) layer-by-layer assembly on silicon wafer. The thickness and refractive index were monitored in real time using discrete wavelength (632.8 nm) ellipsometer and refractive index. From Clausius-Mosseti equation, we can derive the relation between refractive index, film thickness, and temperature.
Keywords: Layer-by-layer, poly(allylamine hydrochloride), poly(acrylic acid)

25. Xu; Yury Yarovoy, Eric Dufresne

Yale University, Unilever R&D

"Imaging micro-stress in drying soap films"

Keywords: Micro-stress, traction force microscopy, drying, soap

top of page