22 research outputs found
Anomalous Microfluidic Phonons Induced by the Interplay of Hydrodynamic Screening and Incompressibility
We investigate the acoustic normal modes ("phonons") of a 1D microfluidic
droplet crystal at the crossover between 2D flow and confined 1D plug flow. The
unusual phonon spectra of the crystal, which arise from long-range hydrodynamic
interactions, change anomalously under confinement. The boundaries induce
weakening and screening of the interactions, but when approaching the 1D limit
we measure a marked increase in the crystal sound velocity, a sign of
interaction strengthening. This non-monotonous behavior of the phonon spectra
is explained theoretically by the interplay of screening and plug flow.Comment: http://link.aps.org/doi/10.1103/PhysRevLett.99.124502
http://www.weizmann.ac.il/complex/tlusty/papers/PhysRevLett2007.pd
Cellular heterogeneity mediates inherent sensitivity–specificity tradeoff in cancer targeting by synthetic circuits
Synthetic gene circuits are emerging as a versatile means to target cancer with enhanced specificity by combinatorial integration of multiple expression markers. Such circuits must also be tuned to be highly sensitive because escape of even a few cells might be detrimental. However, the error rates of decision-making circuits in light of cellular variability in gene expression have so far remained unexplored. Here, we measure the single-cell response function of a tunable logic AND gate acting on two promoters in heterogeneous cell populations. Our analysis reveals an inherent tradeoff between specificity and sensitivity that is controlled by the AND gate amplification gain and activation threshold. We implement a tumor-mimicking cellculture model of cancer cells emerging in a background of normal ones, and show that molecular parameters of the synthetic circuits control specificity and sensitivity in a killing assay. This suggests that, beyond the inherent tradeoff, synthetic circuits operating in a heterogeneous environment could be optimized to efficiently target malignant state with minimal loss of specificity. Keywords: synthetic gene circuits; cellular heterogeneity; cancer gene therapy; cell-state targeting; mammalian synthetic biolog
Phonons in a one-dimensional microfluidic crystal
The development of a general theoretical framework for describing the
behaviour of a crystal driven far from equilibrium has proved difficult1.
Microfluidic crystals, formed by the introduction of droplets of immiscible
fluid into a liquid-filled channel, provide a convenient means to explore and
develop models to describe non-equilibrium dynamics2, 3, 4, 5, 6, 7, 8, 9, 10,
11. Owing to the fact that these systems operate at low Reynolds number (Re),
in which viscous dissipation of energy dominates inertial effects, vibrations
are expected to be over-damped and contribute little to their dynamics12, 13,
14. Against such expectations, we report the emergence of collective normal
vibrational modes (equivalent to acoustic 'phonons') in a one-dimensional
microfluidic crystal of water-in-oil droplets at Reapprox10-4. These phonons
propagate at an ultra-low sound velocity of approx100 mum s-1 and frequencies
of a few hertz, exhibit unusual dispersion relations markedly different to
those of harmonic crystals, and give rise to a variety of crystal instabilities
that could have implications for the design of commercial microfluidic systems.
First-principles theory shows that these phonons are an outcome of the
symmetry-breaking flow field that induces long-range inter-droplet
interactions, similar in nature to those observed in many other systems
including dusty plasma crystals15, 16, vortices in superconductors17, 18,
active membranes19 and nucleoprotein filaments20.Comment: https://www.weizmann.ac.il/complex/tlusty/papers/NaturePhys2006.pd
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The human body at cellular resolution: the NIH Human Biomolecular Atlas Program
Abstract: Transformative technologies are enabling the construction of three-dimensional maps of tissues with unprecedented spatial and molecular resolution. Over the next seven years, the NIH Common Fund Human Biomolecular Atlas Program (HuBMAP) intends to develop a widely accessible framework for comprehensively mapping the human body at single-cell resolution by supporting technology development, data acquisition, and detailed spatial mapping. HuBMAP will integrate its efforts with other funding agencies, programs, consortia, and the biomedical research community at large towards the shared vision of a comprehensive, accessible three-dimensional molecular and cellular atlas of the human body, in health and under various disease conditions
The physics of 2D microfluidic droplet ensembles
We review non-equilibrium many-body phenomena in ensembles of 2D microfluidic droplets. The system comprises of continuous two-phase flow with disc-shaped droplets driven in a channel, at low Reynolds number of 10(-4)-10(-3). The basic physics is that of an effective potential flow, governed by the 2D Laplace equation, with multiple, static and dynamic, boundaries of the droplets and the walls. The motion of the droplets induces dipolar flow fields, which mediated 1/r(2) hydrodynamic interaction between the droplets. Summation of these long-range 2D forces over droplet ensembles converges, in contrast to the divergence of the hydrodynamic forces in 3D. In analogy to electrostatics, the strong effect of boundaries on the equations of motion is calculated by means of image dipoles. We first consider the dynamics of droplets flowing in a 1D crystal, which exhibits unique phonon-like excitations, and a variety of nonlinear instabilities-all stemming from the hydrodynamic interactions. Narrowing the channel results in hydrodynamic screening of the dipolar interactions, which changes salient features of the phonon spectra. Shifting from a 1D ordered crystal to 2D disordererd ensemble, the hydrodynamic interactions induce collective density waves and shocks, which are superposed on single-droplet randomized motion and dynamic clustering. These collective modes originate from density-velocity coupling, whose outcome is a 1D Burgers equation. The rich observational phenomenology and the tractable theory render 2D droplet ensembles a suitable table-top system for studying non-equilibrium many-body physics with long-range interactions
Dendritic and Nanowire Assemblies of Condensed DNA Polymer Brushes
We
investigated the collective conformational response of DNA polymer
brushes to condensation induced by the trivalent cation spermidine.
DNA brushes, a few kilobase-pairs long, undergo a striking transition
into macroscopic domains of collapsed chains with fractal dendritic
morphology. Condensation is initiated by focal nucleation of a towerlike
bundle, which laterally expands in a chain-reaction cascade of structural
chain-to-chain collapse onto the surface. The transition exhibits
the hallmarks of a first-order phase transition with grain boundaries,
hysteresis, and coexistence between condensed and uncondensed phases.
We found that an extended DNA conformation is maintained throughout
the transition and is a prerequisite for the formation of large-scale
dendritic domains. We identified a critical DNA density above which
the nucleation propensity and growth rate sharply increase. We hypothesize
that the ability of DNA-scaffolding proteins to modify the local DNA
density within a genome may act as a dynamic and sensitive mechanism
for spatial regulation of DNA transactions in vivo by selective condensation
of chromosomal territories. By assembling a DNA brush along a patterned
line narrower than twice the DNA contour length and tuning the local
surface densities, we were able to initiate nucleation at a predefined
location and induced growth of a single condensed nanowire over a
distance 2 orders of magnitude longer than the single-chain contour.
Our results demonstrate spatial control of condensation as a new tool
for constructing DNA-based synthetic systems with important implications
for regulation of DNA transactions on surfaces
Dendritic and Nanowire Assemblies of Condensed DNA Polymer Brushes
We
investigated the collective conformational response of DNA polymer
brushes to condensation induced by the trivalent cation spermidine.
DNA brushes, a few kilobase-pairs long, undergo a striking transition
into macroscopic domains of collapsed chains with fractal dendritic
morphology. Condensation is initiated by focal nucleation of a towerlike
bundle, which laterally expands in a chain-reaction cascade of structural
chain-to-chain collapse onto the surface. The transition exhibits
the hallmarks of a first-order phase transition with grain boundaries,
hysteresis, and coexistence between condensed and uncondensed phases.
We found that an extended DNA conformation is maintained throughout
the transition and is a prerequisite for the formation of large-scale
dendritic domains. We identified a critical DNA density above which
the nucleation propensity and growth rate sharply increase. We hypothesize
that the ability of DNA-scaffolding proteins to modify the local DNA
density within a genome may act as a dynamic and sensitive mechanism
for spatial regulation of DNA transactions in vivo by selective condensation
of chromosomal territories. By assembling a DNA brush along a patterned
line narrower than twice the DNA contour length and tuning the local
surface densities, we were able to initiate nucleation at a predefined
location and induced growth of a single condensed nanowire over a
distance 2 orders of magnitude longer than the single-chain contour.
Our results demonstrate spatial control of condensation as a new tool
for constructing DNA-based synthetic systems with important implications
for regulation of DNA transactions on surfaces
Computational analysis of protein synthesis, diffusion, and binding in compartmental biochips
Abstract Protein complex assembly facilitates the combination of individual protein subunits into functional entities, and thus plays a crucial role in biology and biotechnology. Recently, we developed quasi-twodimensional, silicon-based compartmental biochips that are designed to study and administer the synthesis and assembly of protein complexes. At these biochips, individual protein subunits are synthesized from locally confined high-density DNA brushes and are captured on the chip surface by molecular traps. Here, we investigate single-gene versions of our quasi-twodimensional synthesis systems and introduce the trap-binding efficiency to characterize their performance. We show by mathematical and computational modeling how a finite trap density determines the dynamics of protein-trap binding and identify three distinct regimes of the trap-binding efficiency. We systematically study how protein-trap binding is governed by the system’s three key parameters, which are the synthesis rate, the diffusion constant and the trap-binding affinity of the expressed protein. In addition, we describe how spatially differential patterns of traps modulate the protein-trap binding dynamics. In this way, we extend the theoretical knowledge base for synthesis, diffusion, and binding in compartmental systems, which helps to achieve better control of directed molecular self-assembly required for the fabrication of nanomachines for synthetic biology applications or nanotechnological purposes
Collective Conformations of DNA Polymers Assembled on Surface Density Gradients
To study dense double-stranded DNA (dsDNA) polymer phases,
we fabricated
continuous density gradients of binding sites for assembly on a photochemical
interface and measured both dsDNA occupancy and extension using evanescent
fluorescence. Despite the abundance of available binding sites, the
dsDNA density saturates after occupation of only a fraction of the
available sites along the gradient. The spatial position at which
the density saturates marks the onset of collective stretching of
dsDNA, a direct manifestation of balancing entropic and excluded-volume
interactions. The methodology presented here offers a new means to
investigate dense dsDNA compartments