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@APSphysics's interdisciplinary journal for quantitative biological research - the first of its kind and #OpenAccess.
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ALT Schematic of the broadcasting model. The label at the top says “input transcription factor (TF).” A circle at the top of the figure is labeled with “c.” From the top circle, four long arrows point down to circles at the bottom. From left to right, the circles are labeled “g1,” “g2,” and “g3.” A long dashed line separates those three circles from the fourth, which is labeled “gm.” At the bottom, a label reads “output genes {gi}."
ALT A schematic displaying two parallel DNA duplexes to illustrate helical coherence theory. The two DNA strands are colored blue and red, and are outlined with solid black lines as well as a black dashed line tracing the interior helical structure. On the left, black arrows label the minor groove, major groove, and phosphates in the duplex. A black horizontal line labeled “R” indicates the interaxial separation between the duplexes, while a shorter vertical line in between the duplexes denotes the axial shift. At the bottom, an equation indicates the relative azimuthal orientation of the DNA duplexes.
ALT A two-panel diagram comparing Complex Environments and Simple Environments. In the complex panel, a jagged multicolored line graph sits beside a line drawing of a bacterium surrounded by colorful circles, triangles, and other shapes. In the simple panel, a flat pink line graph sits beside a line drawing of a bacterium surrounded only by identical pink circles. Below each panel, an arrow labeled 'Evolution' points to Controllability up, Thermodynamic Cost up for the complex panel, and Controllability down, Thermodynamic Cost down for the simple panel. At the bottom, a pink gear represents ATP and a blue gear represents GTP. The two gears are similarly sized in the complex panel, with one gear much larger than the other in the simple panel.
ALT Three side-by-side, simple geometric schematics visualizing the architectures tested in the study. The schematics portray modularized (orange, left), fully connected (red, center), and bottleneck (purple, right) architectures. In each schematic, each circle represents a single neuron unit, and the rectangles represent a group of neurons. The circles are labeled x1, x2, y, z1, or z2 in each schematic. At the bottom, a line of text portrays the equation for learning of 2-input, 1-output functions.
ALT A three-part figure. At top: four illustrations showing pink assembly factors surrounding orange protein subunits as they come together from scattered pieces into a large cluster. A time arrow is below. At bottom left: two cryoEM images of a yeast ribosome large subunit, each with gray/white RNA with orange protein regions and pink assembly-factor regions. At the bottom right: two cryoEM images showing orange protein masses with small pink assembly-factor regions.
ALT An illustration of actin networks grown from beads with either high, shown in blue, or low, shown in orange, coating densities of nucleation promoting factor that coexist in a shared pool of actin monomers. The image shows how the strong beads create denser networks than the weak beads and consume more monomers per time.
ALT A three-part scientific diagram. The top panel is labeled stochastic environment and shows a square-wave line that alternates between peaks in green labeled “good” and troughs in red labeled “bad.” The middle section features a blue box on the left labeled “reproduction through inactive propagules.” It shows a green plant icon and an arrow that points to a purple seed icon. An arrow labeled “delay alpha” connects the blue box to a yellow box on the right. The yellow box is labeled “activation” and shows a purple seed icon and an arrow that points to a plant icon. The bottom section features a graph with delay alpha on the x-axis and distribution on the y-axis. It depicts three curves. From left to right there is a green curve labeled “short” in the center and “adaptive” above, a red curve labeled “intermediate” in the center and “maladaptive” above, and a green curve labeled “long” in the center and “adaptive” above.
ALT Antibody/nanobody complex predictions given by an existing prediction model on the left and the new approach on the right. The predictions look like tangled, curly pieces of twine colored salmon, blue, and gray, with silhouettes along the perimeters. The gray represents experimental structures, the salmon and blue are predictions, and the silhouettes are lower-ranked predictions. There is more overlap between the predicted structures and experimental structures in the output on the right — the new approach — and more lower-ranked predictions in general.
ALT A simple infographic shows the conceptual framework of condensation, delineating various control parameters that affect condensate properties. To the left, a column of blue rectangles lists control parameters including intermolecular affinities, molecular concentration, intracellular structures, physical fields and extrinsic stimuli, and active processes. To the right, a column of darker blue rectangles lists condensate properties including composition, location, timing, material properties, internal organization, and morphology.
ALT A visual representation of the formation of compact heterochromatic regions. The first panel on the top left shows spatially separated heterochromatin, which look like blue and yellow balls. The second panel on the top right, which occurs later in time, shows a more condensed set of heterochromatin and enzymes. The third panel on the bottom has merged into an even larger, merged set of heterochromatin and enzymes.
ALT A series of nine black-and-white and color-labeled confocal microscopy images of condensates rich in polyethylene glycol, housed in phosphate buffer solutions of varying pH levels. The condensates appear as dots of circles that accumulate into one large circular structure as the buffer pH rises from left to right: 6.9 (left), 7 (middle), and 7.8 (right). The top row of images corresponds to maximum intensity projections of the condensates. The middle row shows a representative xz section of the image stack. The bottom row shows segmentation of the condensates, which are colored according to a color scale bar that denotes intensity ranging from dark blue at the lowest values to white at the highest.
ALT Images showing the multiple particle tracking of chromatin loci and event-conditioned mobility pathways. On the bottom right corner is an image of a gray oval shape labeled detected chromatic loci. It shows how chromatin granules, indicated with red markers, are detected in live, unstained interphase nuclei and tracked over time. An arrow points from one granule upwards to show how these data then yield single-locus Brownian trajectories, shown as a series of squiggly rainbow-colored lines with time on the x axis and MSD on the y axis. Below and to the left is a schematic showing how rare transitions between low- and high-mobility states are used to define event-aligned histograms of MSD evolution that provides a structured description of activation, shown in red, and reconfinement, shown in blue, pathways that complements standard time-averaged diffusion summaries.
ALT An illustration showing the parameters governing ant interactions in the model. On the top is a depiction of the sensing area and two example interactions, labeled connected and not connected, between two ants. Below, over a bout of movement, an individual is shown as being capable of interacting with other ants in the domain spanned by its duration-specific area coverage, shown in red. The study neglects the edge of the area coverage, shown in blue, by assuming it is small in comparison to the movement bout.
ALT A graph showing respiratory frequency in Hertz on the x-axis and air sac pressure response on the y-axis. A dashed line that drops quickly from its peak at y = 1 is labeled quiet. A solid line and dots that follow a slower decrease from y = 1 is labeled song. A cartoon of a canary next to two music notes is in the top right corner.
ALT Images of individual heterotypic 10A and TSA-treated 10A spheroids with actin, shown in green, and CellTracker-Orange labeled TSA-treated 10A cells, shown in orange. A spheroid on the left contains 75% 10A cells and 25% TSA-treated 10A cells. A spheroid on the right contains 25% 10A cells and 75% TSA-treated 10A cells. The two images show that as the proportion of TSA-treated 10A cells increases, fusion increases. The scale bar shows 100 micrometers. The inset in each image displays the corresponding fusion of heterotypic 10A/TSA-treated 10A spheroids after 50 hours of fusion. The scale bar in the inset image is 200 micrometers.