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result(s) for
"Fraden, Seth"
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Turbulent beginnings
2019
An inspired experimental approach sheds light on the formation of active turbulence in a system of microtubules and molecular motors. The emergent scaling behaviour takes us a step closer to understanding how activity begets turbulence.
Journal Article
Programmable icosahedral shell system for virus trapping
by
Hagan, Michael F.
,
Wilsch, Florian
,
Sigl, Christian
in
631/57/2282
,
631/61/338/552
,
631/61/350
2021
Broad-spectrum antiviral platforms that can decrease or inhibit viral infection would alleviate many threats to global public health. Nonetheless, effective technologies of this kind are still not available. Here, we describe a programmable icosahedral canvas for the self-assembly of icosahedral shells that have viral trapping and antiviral properties. Programmable triangular building blocks constructed from DNA assemble with high yield into various shell objects with user-defined geometries and apertures. We have created shells with molecular masses ranging from 43 to 925 MDa (8 to 180 subunits) and with internal cavity diameters of up to 280 nm. The shell interior can be functionalized with virus-specific moieties in a modular fashion. We demonstrate this virus-trapping concept by engulfing hepatitis B virus core particles and adeno-associated viruses. We demonstrate the inhibition of hepatitis B virus core interactions with surfaces in vitro and the neutralization of infectious adeno-associated viruses exposed to human cells.
Programmable triangular DNA blocks self-assemble into distinct icosahedral shells with specific geometry and apertures that can encapsulate viruses and decrease viral infection.
Journal Article
Self-organized dynamics and the transition to turbulence of confined active nematics
by
Opathalage, Achini
,
Langeslay, Blake
,
Aghvami, S. Ali
in
active matter
,
Applied Physical Sciences
,
Circularity
2019
We study how confinement transforms the chaotic dynamics of bulk microtubule-based active nematics into regular spatiotemporal patterns. For weak confinements in disks, multiple continuously nucleating and annihilating topological defects self-organize into persistent circular flows of either handedness. Increasing confinement strength leads to the emergence of distinct dynamics, in which the slow periodic nucleation of topological defects at the boundary is superimposed onto a fast procession of a pair of defects. A defect pair migrates toward the confinement core over multiple rotation cycles, while the associated nematic director field evolves from a distinct double spiral toward a nearly circularly symmetric configuration. The collapse of the defect orbits is punctuated by another boundary-localized nucleation event, that sets up long-term doubly periodic dynamics. Comparing experimental data to a theoretical model of an active nematic reveals that theory captures the fast procession of a pair of +1/2 defects, but not the slow spiral transformation nor the periodic nucleation of defect pairs. Theory also fails to predict the emergence of circular flows in the weak confinement regime. The developed confinement methods are generalized to more complex geometries, providing a robust microfluidic platform for rationally engineering 2D autonomous flows.
Journal Article
Transition from turbulent to coherent flows in confined three-dimensional active fluids
by
Chen, Daniel T. N.
,
DeCamp, Stephen J.
,
Dogic, Zvonimir
in
Adenosine triphosphate
,
Aspect ratio
,
Biological effects
2017
The transport of ordinary fluids tends to be driven by pressure differentials, whereas for active or biological matter, transport may be isotropic or governed by the presence of specific chemical gradients. Wu et al. analyzed the emergence of spontaneous directional flows in active fluids containing a suspension of microtubules and clusters of the molecular motor kinesin, confined in a variety of microfluidic geometries (see the Perspective by Morozov). When confined in periodic toroidal channels and cylindrical domains, the flow was organized and persisted in a unidirectional motion, either clockwise or counterclockwise. Oddly, this behavior was independent of scale; as long as the aspect ratio of the geometry was chosen appropriately, flows were observed for a wide range of system dimensions. Science , this issue p. eaal1979 ; see also p. 1262 An isotropic fluid composed of nanosized motors organizes into an autonomous machine that pumps fluid through long channels. Transport of fluid through a pipe is essential for the operation of macroscale machines and microfluidic devices. Conventional fluids only flow in response to external pressure. We demonstrate that an active isotropic fluid, composed of microtubules and molecular motors, autonomously flows through meter-long three-dimensional channels. We establish control over the magnitude, velocity profile, and direction of the self-organized flows and correlate these to the structure of the extensile microtubule bundles. The inherently three-dimensional transition from bulk-turbulent to confined-coherent flows occurs concomitantly with a transition in the bundle orientational order near the surface and is controlled by a scale-invariant criterion related to the channel profile. The nonequilibrium transition of confined isotropic active fluids can be used to engineer self-organized soft machines.
Journal Article
Submersed micropatterned structures control active nematic flow, topology, and concentration
by
Aghvami, S. Ali
,
Shendruk, Tyler N.
,
Khaladj, Dimitrius A.
in
Active control
,
Control methods
,
Coupling
2021
Coupling between flows and material properties imbues rheological matter with its wide-ranging applicability, hence the excitement for harnessing the rheology of active fluids for which internal structure and continuous energy injection lead to spontaneous flows and complex, out-of-equilibrium dynamics.We propose and demonstrate a convenient, highly tunable method for controlling flow, topology, and composition within active films. Our approach establishes rheological coupling via the indirect presence of fully submersed micropatterned structures within a thin, underlying oil layer. Simulations reveal that micropatterned structures produce effective virtual boundaries within the superjacent active nematic film due to differences in viscous dissipation as a function of depth. This accessible method of applying position-dependent, effective dissipation to the active films presents a nonintrusive pathway for engineering active microfluidic systems.
Journal Article
Testing Turing's theory of morphogenesis in chemical cells
2014
Alan Turing, in \"The Chemical Basis of Morphogenesis\" [Turing AM (1952) Philos Trans R Soc Lond 237(641):37—72], described how, in circular arrays of identical biological cells, diffusion can interact with chemical reactions to generate up to six periodic spatiotemporal chemical structures. Turing proposed that one of these structures, a stationary pattern with a chemically determined wavelength, is responsible for differentiation. We quantitatively test Turing's ideas in a cellular chemical system consisting of an emulsion of aqueous droplets containing the Belousov—Zhabotinsky oscillatory chemical reactants, dispersed in oil, and demonstrate that reaction-diffusion processes lead to chemical differentiation, which drives physical morphogenesis in chemical cells. We observe five of the six structures predicted by Turing. In 2D hexagonal arrays, a seventh structure emerges, incompatible with Turing's original model, which we explain by modifying the theory to include heterogeneity.
Journal Article
An Arduino-based constant pressure fluid pump
by
Lupinski, Theodore
,
Ludwig, Markus
,
Tompkins, Nathan
in
Biological and Medical Physics
,
Biophysics
,
Chemical reactions
2021
Constant pressure pumps are an invaluable yet underutilized resource for microfluidic flow systems. In particular, constant pressure pumps are able to stabilize the fluid pressure in systems where the viscosity may change due to chemical reactions or the flow rate may vary due to deformations of the channels. The constant pressure pump presented here is designed on the premise of creating and maintaining a pressure differential between the laboratory and a pressure reservoir. This pressure reservoir is then used to drive the input fluid at the specified gauge pressure. The pump design presented here is perfect for primarily undergraduate institutions and other laboratories with modest research budgets as it can be built for under US$100 and construction is within the scope of an advanced undergraduate. The pump consists of an Arduino-compatible microcontroller, Adafruit electronic components, low-voltage air pump, Nalgene water bottle, and various fluid components. A complete parts list is included in the appendix. Comparable commercial pumps have a retail price in excess of US$5000. Multiple pump designs were constructed and tested with the ability to hold a constant pressure of up to 14 psig (97 kPa-gauge) with a maximum flow rate of 65
μ
L/s for water.
Graphic abstract
Journal Article
Modular programming of interaction and geometric specificity enables assembly of complex DNA origami nanostructures
by
Price, Mason
,
Pombo, Juanita
,
Arya, Gaurav
in
631/57/2282
,
639/925/926/1049
,
Anisotropic shells
2025
Self-assembly of nanoscale building blocks with programmable geometries and interactions offers a powerful route to engineer materials that mimic the complexity of biological structures. DNA origami provides an exceptional platform for this purpose, enabling precise control over subunit shape, binding angles, and interaction specificity. Here we present a modular DNA origami design approach to address the challenges of assembling geometrically complex nanoscale structures, including those with nonuniform curvatures. This approach features a core structure that completely conserves the scaffold routing across different designs and preserves more than 70% of the DNA staples between designs, dramatically reducing both cost and effort, while enabling precise and independent programming of subunit interactions and binding angles through adjustable overhang lengths and sequences. Using cryogenic electron microscopy, gel electrophoresis, and coarse-grained simulations, we validate a set of robust design rules and demonstrate the assembly of diverse self-limiting structures, including anisotropic shells, a
T
= 13 icosahedral shell, and a toroid with globally varying curvature. This modular strategy provides an efficient and cost-effective framework for the synthetic fabrication of complex nanostructures.
DNA origami enables precise nanoscale self-assembly. Authors here show how programmable control of interactions and binding angles yields curved surfaces of diverse geometries, broadening the design space for synthetic nanostructures.
Journal Article
Room-temperature serial crystallography using a kinetically optimized microfluidic device for protein crystallization and on-chip X-ray diffraction
by
Akella, Sathish
,
Szebenyi, Doletha M. E.
,
Heymann, Michael
in
Chemical engineering
,
Chemical engineering research
,
Crystallization
2014
An emulsion-based serial crystallographic technology has been developed, in which nanolitre-sized droplets of protein solution are encapsulated in oil and stabilized by surfactant. Once the first crystal in a drop is nucleated, the small volume generates a negative feedback mechanism that lowers the supersaturation. This mechanism is exploited to produce one crystal per drop. Diffraction data are measured, one crystal at a time, from a series of room-temperature crystals stored on an X-ray semi-transparent microfluidic chip, and a 93% complete data set is obtained by merging single diffraction frames taken from different unoriented crystals. As proof of concept, the structure of glucose isomerase was solved to 2.1 Å, demonstrating the feasibility of high-throughput serial X-ray crystallography using synchrotron radiation.
Journal Article
Entropically driven microphase transitions in mixtures of colloidal rods and spheres
by
Dogic, Zvonimir
,
Adams, Marie
,
Keller, Sarah L.
in
Chemistry
,
Colloidal state and disperse state
,
Entropy
1998
Although the idea that entropy alone is sufficient to produce an ordered state is an old one in colloid science
1
, the notion remains counter-intuitive and it is often assumed that attractive interactions are necessary to generate phases with long-range order. The phase behaviour for both rods and spheres has been studied experimentally
1
,
2
,
3
,
4
,
5
,
6
,
7
, theoretically
8
,
9
and by computer simulations
10
. Here we describe the phase behaviour of mixtures of colloidal rod-like and sphere-like particles (respectively viruses and polystyrene latex or polyethylene oxide polymer) under conditions in which they act like hard' particles
2
,
3
. We find a wealth of behaviour: bulk demixing into rod-rich and rod-poor phases and microphase separation into a variety of morphologies. One microphase consists of layers of rods alternating with layers of spheres
11
; in another microphase of unanticipated complexity, the spheres reversibly assemble into columns, which in turn pack into a crystalline array. Our experiments, and previous theory and computer simulations
11
, suggest that this phase behaviour is entropically driven by steric repulsion between particles. The phenomena are likely to be quite general, applying also for example to low-molecular-mass liquid crystals
12
. This kind of microphase separation might also be relevant to systems of amphiphiles
13
and block copolymers
14
, to bioseparation methods and DNA partitioning in prokaryotes
15
, and to protein crystallization
16
,
17
and the manufacture of composite materials.
Journal Article