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  • 1
    In: Nature, Springer Science and Business Media LLC, Vol. 551, No. 7678 ( 2017-11-02), p. 92-94
    Type of Medium: Online Resource
    ISSN: 0028-0836 , 1476-4687
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    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2017
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    detail.hit.zdb_id: 1413423-8
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  • 2
    Online Resource
    Online Resource
    Proceedings of the National Academy of Sciences ; 2007
    In:  Proceedings of the National Academy of Sciences Vol. 104, No. 43 ( 2007-10-23), p. 16998-17003
    In: Proceedings of the National Academy of Sciences, Proceedings of the National Academy of Sciences, Vol. 104, No. 43 ( 2007-10-23), p. 16998-17003
    Abstract: Physiological and evolutionary adaptations operate at very different time scales. Nevertheless, there are reasons to believe there should be a strong relationship between the two, as together they modify the phenotype. Physiological adaptations change phenotype by altering certain microscopic parameters; evolutionary adaptation can either alter genetically these same parameters or others to achieve distinct or similar ends. Although qualitative discussions of this relationship abound, there has been very little quantitative analysis. Here, we use the hemoglobin molecule as a model system to quantify the relationship between physiological and evolutionary adaptations. We compare measurements of oxygen saturation curves of 25 mammals with those of human hemoglobin under a wide range of physiological conditions. We fit the data sets to the Monod–Wyman–Changeux model to extract microscopic parameters. Our analysis demonstrates that physiological and evolutionary change act on different parameters. The main parameter that changes in the physiology of hemoglobin is relatively constant in evolution, whereas the main parameter that changes in the evolution of hemoglobin is relatively constant in physiology. This orthogonality suggests continued selection for physiological adaptability and hints at a role for this adaptability in evolutionary change.
    Type of Medium: Online Resource
    ISSN: 0027-8424 , 1091-6490
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    Language: English
    Publisher: Proceedings of the National Academy of Sciences
    Publication Date: 2007
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  • 3
    Online Resource
    Online Resource
    Proceedings of the National Academy of Sciences ; 2016
    In:  Proceedings of the National Academy of Sciences Vol. 113, No. 41 ( 2016-10-11), p. 11425-11430
    In: Proceedings of the National Academy of Sciences, Proceedings of the National Academy of Sciences, Vol. 113, No. 41 ( 2016-10-11), p. 11425-11430
    Abstract: We propose and experimentally test a method to fabricate patterns of steep, sharp features on surfaces, by exploiting the nonlinear dynamics of uniformly ion-bombarded surfaces. We show via theory, simulation, and experiment that the steepest parts of the surface evolve as one-dimensional curves that move in the normal direction at constant velocity. The curves are a special solution to the nonlinear equations that arises spontaneously whenever the initial patterning on the surface contains slopes larger than a critical value; mathematically they are traveling waves (shocks) that have the special property of being undercompressive. We derive the evolution equation for the curves by considering long-wavelength perturbations to the one-dimensional traveling wave, using the unusual boundary conditions required for an undercompressive shock, and we show this equation accurately describes the evolution of shapes on surfaces, both in simulations and in experiments. Because evolving a collection of one-dimensional curves is fast, this equation gives a computationally efficient and intuitive method for solving the inverse problem of finding the initial surface so the evolution leads to a desired target pattern. We illustrate this method by solving for the initial surface that will produce a lattice of diamonds connected by steep, sharp ridges, and we experimentally demonstrate the evolution of the initial surface into the target pattern.
    Type of Medium: Online Resource
    ISSN: 0027-8424 , 1091-6490
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    Language: English
    Publisher: Proceedings of the National Academy of Sciences
    Publication Date: 2016
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    detail.hit.zdb_id: 1461794-8
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  • 4
    Online Resource
    Online Resource
    American Association for the Advancement of Science (AAAS) ; 2005
    In:  Science Vol. 310, No. 5746 ( 2005-10-14), p. 294-297
    In: Science, American Association for the Advancement of Science (AAAS), Vol. 310, No. 5746 ( 2005-10-14), p. 294-297
    Abstract: We report a regime of ion beam sputtering that occurs for sufficiently steep slopes. High slopes propagate over large distances without dissipating the steepest features. Both the propagation velocity and the dynamically selected slope are universal, independent of the details of the initial shape of the surface. The resulting behavior can be understood as the propagation of a shock front that self-selects a stable slope, as has been previously observed in thin-film fluid flows. Experiments confirm predictions of the theory. An important implication of the propagative behavior at high surface slopes is that a pattern can be fabricated at a large length scale and, through uniform ion irradiation, reduced to a smaller length scale while preserving, or even sharpening, the sharpest features.
    Type of Medium: Online Resource
    ISSN: 0036-8075 , 1095-9203
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    Language: English
    Publisher: American Association for the Advancement of Science (AAAS)
    Publication Date: 2005
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  • 5
    Online Resource
    Online Resource
    Proceedings of the National Academy of Sciences ; 2013
    In:  Proceedings of the National Academy of Sciences Vol. 110, No. 3 ( 2013-01-15), p. 848-852
    In: Proceedings of the National Academy of Sciences, Proceedings of the National Academy of Sciences, Vol. 110, No. 3 ( 2013-01-15), p. 848-852
    Abstract: Many bacteria on earth exist in surface-attached communities known as biofilms. These films are responsible for manifold problems, including hospital-acquired infections and biofouling, but they can also be beneficial. Biofilm growth depends on the transport of nutrients and waste, for which diffusion is thought to be the main source of transport. However, diffusion is ineffective for transport over large distances and thus should limit growth. Nevertheless, biofilms can grow to be very large. Here we report the presence of a remarkable network of well-defined channels that form in wild-type Bacillus subtilis biofilms and provide a system for enhanced transport. We observe that these channels have high permeability to liquid flow and facilitate the transport of liquid through the biofilm. In addition, we find that spatial variations in evaporative flux from the surface of these biofilms provide a driving force for the flow of liquid in the channels. These channels offer a remarkably simple system for liquid transport, and their discovery provides insight into the physiology and growth of biofilms.
    Type of Medium: Online Resource
    ISSN: 0027-8424 , 1091-6490
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    Language: English
    Publisher: Proceedings of the National Academy of Sciences
    Publication Date: 2013
    detail.hit.zdb_id: 209104-5
    detail.hit.zdb_id: 1461794-8
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  • 6
    Online Resource
    Online Resource
    Proceedings of the National Academy of Sciences ; 2021
    In:  Proceedings of the National Academy of Sciences Vol. 118, No. 10 ( 2021-03-09)
    In: Proceedings of the National Academy of Sciences, Proceedings of the National Academy of Sciences, Vol. 118, No. 10 ( 2021-03-09)
    Abstract: The inverse problem of designing component interactions to target emergent structure is fundamental to numerous applications in biotechnology, materials science, and statistical physics. Equally important is the inverse problem of designing emergent kinetics, but this has received considerably less attention. Using recent advances in automatic differentiation, we show how kinetic pathways can be precisely designed by directly differentiating through statistical physics models, namely free energy calculations and molecular dynamics simulations. We consider two systems that are crucial to our understanding of structural self-assembly: bulk crystallization and small nanoclusters. In each case, we are able to assemble precise dynamical features. Using gradient information, we manipulate interactions among constituent particles to tune the rate at which these systems yield specific structures of interest. Moreover, we use this approach to learn nontrivial features about the high-dimensional design space, allowing us to accurately predict when multiple kinetic features can be simultaneously and independently controlled. These results provide a concrete and generalizable foundation for studying nonstructural self-assembly, including kinetic properties as well as other complex emergent properties, in a vast array of systems.
    Type of Medium: Online Resource
    ISSN: 0027-8424 , 1091-6490
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    Language: English
    Publisher: Proceedings of the National Academy of Sciences
    Publication Date: 2021
    detail.hit.zdb_id: 209104-5
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  • 7
    Online Resource
    Online Resource
    Proceedings of the National Academy of Sciences ; 2017
    In:  Proceedings of the National Academy of Sciences Vol. 114, No. 2 ( 2017-01-10), p. 257-262
    In: Proceedings of the National Academy of Sciences, Proceedings of the National Academy of Sciences, Vol. 114, No. 2 ( 2017-01-10), p. 257-262
    Abstract: Controlling motion at the microscopic scale is a fundamental goal in the development of biologically inspired systems. We show that the motion of active, self-propelled colloids can be sufficiently controlled for use as a tool to assemble complex structures such as braids and weaves out of microscopic filaments. Unlike typical self-assembly paradigms, these structures are held together by geometric constraints rather than adhesive bonds. The out-of-equilibrium assembly that we propose involves precisely controlling the 2D motion of active colloids so that their path has a nontrivial topology. We demonstrate with proof-of-principle Brownian dynamics simulations that, when the colloids are attached to long semiflexible filaments, this motion causes the filaments to braid. The ability of the active particles to provide sufficient force necessary to bend the filaments into a braid depends on a number of factors, including the self-propulsion mechanism, the properties of the filament, and the maximum curvature in the braid. Our work demonstrates that nonequilibrium assembly pathways can be designed using active particles.
    Type of Medium: Online Resource
    ISSN: 0027-8424 , 1091-6490
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    Language: English
    Publisher: Proceedings of the National Academy of Sciences
    Publication Date: 2017
    detail.hit.zdb_id: 209104-5
    detail.hit.zdb_id: 1461794-8
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  • 8
    Online Resource
    Online Resource
    American Association for the Advancement of Science (AAAS) ; 2010
    In:  Science Vol. 327, No. 5965 ( 2010-01-29), p. 560-563
    In: Science, American Association for the Advancement of Science (AAAS), Vol. 327, No. 5965 ( 2010-01-29), p. 560-563
    Abstract: The study of clusters has provided a tangible link between local geometry and bulk condensed matter, but experiments have not yet systematically explored the thermodynamics of the smallest clusters. Here we present experimental measurements of the structures and free energies of colloidal clusters in which the particles act as hard spheres with short-range attractions. We found that highly symmetric clusters are strongly suppressed by rotational entropy, whereas the most stable clusters have anharmonic vibrational modes or extra bonds. Many of these clusters are subsets of close-packed lattices. As the number of particles increases from 6 to 10, we observe the emergence of a complex free-energy landscape with a small number of ground states and many local minima.
    Type of Medium: Online Resource
    ISSN: 0036-8075 , 1095-9203
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    Language: English
    Publisher: American Association for the Advancement of Science (AAAS)
    Publication Date: 2010
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    detail.hit.zdb_id: 2066996-3
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  • 9
    Online Resource
    Online Resource
    Proceedings of the National Academy of Sciences ; 2012
    In:  Proceedings of the National Academy of Sciences Vol. 109, No. 4 ( 2012-01-24), p. 1116-1121
    In: Proceedings of the National Academy of Sciences, Proceedings of the National Academy of Sciences, Vol. 109, No. 4 ( 2012-01-24), p. 1116-1121
    Abstract: Bacterial biofilms are organized communities of cells living in association with surfaces. The hallmark of biofilm formation is the secretion of a polymeric matrix rich in sugars and proteins in the extracellular space. In Bacillus subtilis , secretion of the exopolysaccharide (EPS) component of the extracellular matrix is genetically coupled to the inhibition of flagella-mediated motility. The onset of this switch results in slow expansion of the biofilm on a substrate. Different strains have radically different capabilities in surface colonization: Flagella-null strains spread at the same rate as wild type, while both are dramatically faster than EPS mutants. Multiple functions have been attributed to the EPS, but none of these provides a physical mechanism for generating spreading. We propose that the secretion of EPS drives surface motility by generating osmotic pressure gradients in the extracellular space. A simple mathematical model based on the physics of polymer solutions shows quantitative agreement with experimental measurements of biofilm growth, thickening, and spreading. We discuss the implications of this osmotically driven type of surface motility for nutrient uptake that may elucidate the reduced fitness of the matrix-deficient mutant strains.
    Type of Medium: Online Resource
    ISSN: 0027-8424 , 1091-6490
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    Language: English
    Publisher: Proceedings of the National Academy of Sciences
    Publication Date: 2012
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  • 10
    Online Resource
    Online Resource
    Proceedings of the National Academy of Sciences ; 2003
    In:  Proceedings of the National Academy of Sciences Vol. 100, No. 23 ( 2003-11-11), p. 13259-13263
    In: Proceedings of the National Academy of Sciences, Proceedings of the National Academy of Sciences, Vol. 100, No. 23 ( 2003-11-11), p. 13259-13263
    Abstract: Cells of Escherichia coli under conditions of certain cellular stresses excrete attractants. Cells of chemotactic strains respond to these excreted signaling molecules by moving up their local concentration gradients and forming different types of stable multicellular structures. Multicellular clusters are the simplest among these structures. Fluorescence microscopy was used to characterize the macroscopic properties of the clusters and to track individual E. coli cells in the clusters in real time. A quantitative analysis reveals that the equilibrium cluster size is only weakly dependent on the total number of cells in the cluster. The tumble frequency of an individual cell strongly depends on the position of the cell within the cluster and its direction of movement. In the central region of the cluster, tumbles are strongly suppressed whereas near the edge of the cluster, the tumble frequency is restored for exiting cells, thereby preventing them from leaving the cluster, resulting in the maintenance of sharp cluster boundaries. A simulation based on a model of the sensory memory of E. coli reproduces the experimental data and indicates that the tumble rate and consequently the morphology of the cluster are determined by the sensory memory of cells.
    Type of Medium: Online Resource
    ISSN: 0027-8424 , 1091-6490
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    Language: English
    Publisher: Proceedings of the National Academy of Sciences
    Publication Date: 2003
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    detail.hit.zdb_id: 1461794-8
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