127 research outputs found
Helices at Interfaces
Helically coiled filaments are a frequent motif in nature. In situations
commonly encountered in experiments coiled helices are squeezed flat onto two
dimensional surfaces. Under such 2-D confinement helices form "squeelices" -
peculiar squeezed conformations often resembling looped waves, spirals or
circles. Using theory and Monte-Carlo simulations we illuminate here the
mechanics and the unusual statistical mechanics of confined helices and show
that their fluctuations can be understood in terms of moving and interacting
discrete particle-like entities - the "twist-kinks". We show that confined
filaments can thermally switch between discrete topological twist quantized
states, with some of the states exhibiting dramatically enhanced
circularization probability while others displaying surprising
hyperflexibility
Kinematics of the swimming of Spiroplasma
\emph{Spiroplasma} swimming is studied with a simple model based on
resistive-force theory. Specifically, we consider a bacterium shaped in the
form of a helix that propagates traveling-wave distortions which flip the
handedness of the helical cell body. We treat cell length, pitch angle, kink
velocity, and distance between kinks as parameters and calculate the swimming
velocity that arises due to the distortions. We find that, for a fixed pitch
angle, scaling collapses the swimming velocity (and the swimming efficiency) to
a universal curve that depends only on the ratio of the distance between kinks
to the cell length. Simultaneously optimizing the swimming efficiency with
respect to inter-kink length and pitch angle, we find that the optimal pitch
angle is 35.5 and the optimal inter-kink length ratio is 0.338, values
in good agreement with experimental observations.Comment: 4 pages, 5 figure
Twirling Elastica: Kinks, Viscous Drag, and Torsional Stress
Biological filaments such as DNA or bacterial flagella are typically curved
in their natural states. To elucidate the interplay of viscous drag, twisting,
and bending in the overdamped dynamics of such filaments, we compute the
steady-state torsional stress and shape of a rotating rod with a kink. Drag
deforms the rod, ultimately extending or folding it depending on the kink
angle. For certain kink angles and kink locations, both states are possible at
high rotation rates. The agreement between our macroscopic experiments and the
theory is good, with no adjustable parameters.Comment: 4 pages, 4 figure
The role of body rotation in bacterial flagellar bundling
In bacterial chemotaxis, E. coli cells drift up chemical gradients by a
series of runs and tumbles. Runs are periods of directed swimming, and tumbles
are abrupt changes in swimming direction. Near the beginning of each run, the
rotating helical flagellar filaments which propel the cell form a bundle. Using
resistive-force theory, we show that the counter-rotation of the cell body
necessary for torque balance is sufficient to wrap the filaments into a bundle,
even in the absence of the swirling flows produced by each individual filament
Beating patterns of filaments in viscoelastic fluids
Many swimming microorganisms, such as bacteria and sperm, use flexible
flagella to move through viscoelastic media in their natural environments. In
this paper we address the effects a viscoelastic fluid has on the motion and
beating patterns of elastic filaments. We treat both a passive filament which
is actuated at one end, and an active filament with bending forces arising from
internal motors distributed along its length. We describe how viscoelasticity
modifies the hydrodynamic forces exerted on the filaments, and how these
modified forces affect the beating patterns. We show how high viscosity of
purely viscous or viscoelastic solutions can lead to the experimentally
observed beating patterns of sperm flagella, in which motion is concentrated at
the distal end of the flagella
Effects of Microgravity or Simulated Launch on Testicular Function in Rats
Testes from flight rats on COSMOS 2044 and simulated-launch, vivarium, or caudal-elevation control rats (5/group) were analyzed by subjective and quantitative methods. On the basis of observations of fixed tissue, it was evident that some rats had testicular abnormalities unassociated with treatment and probably existing when they were assigned randomly to the four treatment groups. Considering rats without preexisting abnormalities, diameter of seminiferous tubules and numbers of germ cells per tubule cross section were lower (P less than 0.05) in flight than in simulated-launch or vivarium rats. However, ratios of germ cells to each other or to Sertoli cells and number of homogenization-resistant spermatids did not differ from values for simulated-launch or vivarium controls. Expression of testis-specific gene products was not greatly altered by flight. Furthermore, there was no evidence for production of stress-inducible transcripts of the hsp7O or hsp9O genes. Concentration of receptors for rat luteinizing hormone in testicular tissue and surface density of smooth endoplasmic reticulum in Leydig cells were similar in flight and simulated-launch rats. However, concentrations of testosterone in testicular tissue or peripheral blood plasma were reduced (P less than 0.05) in flight rats to less than 20% of values for simulated-launch or vivarium controls. Thus spermatogenesis was essentially normal in flight rats, but production of testosterone was severely depressed. Exposure to microgravity for more than 2 wk might result in additional changes. Sequelae of reduced androgen production associated with microgravity on turnover of muscle and bone should be considered
Twirling and Whirling: Viscous Dynamics of Rotating Elastica
Motivated by diverse phenomena in cellular biophysics, including bacterial
flagellar motion and DNA transcription and replication, we study the overdamped
nonlinear dynamics of a rotationally forced filament with twist and bend
elasticity. Competition between twist injection, twist diffusion, and writhing
instabilities is described by a novel pair of coupled PDEs for twist and bend
evolution. Analytical and numerical methods elucidate the twist/bend coupling
and reveal two dynamical regimes separated by a Hopf bifurcation: (i)
diffusion-dominated axial rotation, or twirling, and (ii) steady-state
crankshafting motion, or whirling. The consequences of these phenomena for
self-propulsion are investigated, and experimental tests proposed.Comment: To be published in Physical Review Letter
Possible origins of macroscopic left-right asymmetry in organisms
I consider the microscopic mechanisms by which a particular left-right (L/R)
asymmetry is generated at the organism level from the microscopic handedness of
cytoskeletal molecules. In light of a fundamental symmetry principle, the
typical pattern-formation mechanisms of diffusion plus regulation cannot
implement the "right-hand rule"; at the microscopic level, the cell's
cytoskeleton of chiral filaments seems always to be involved, usually in
collective states driven by polymerization forces or molecular motors. It seems
particularly easy for handedness to emerge in a shear or rotation in the
background of an effectively two-dimensional system, such as the cell membrane
or a layer of cells, as this requires no pre-existing axis apart from the layer
normal. I detail a scenario involving actin/myosin layers in snails and in C.
elegans, and also one about the microtubule layer in plant cells. I also survey
the other examples that I am aware of, such as the emergence of handedness such
as the emergence of handedness in neurons, in eukaryote cell motility, and in
non-flagellated bacteria.Comment: 42 pages, 6 figures, resubmitted to J. Stat. Phys. special issue.
Major rewrite, rearranged sections/subsections, new Fig 3 + 6, new physics in
Sec 2.4 and 3.4.1, added Sec 5 and subsections of Sec
Experimentally Guided Computational Model Discovers Important Elements for Social Behavior in Myxobacteria
Identifying essential factors in cellular interactions and organized movement of cells is important in predicting behavioral phenotypes exhibited by many bacterial cells. We chose to study Myxococcus xanthus, a soil bacterium whose individual cell behavior changes while in groups, leading to spontaneous formation of aggregation center during the early stage of fruiting body development. In this paper, we develop a cell-based computational model that solely relies on experimentally determined parameters to investigate minimal elements required to produce the observed social behaviors in M. xanthus. The model verifies previously known essential parameters and identifies one novel parameter, the active turning, which we define as the ability and tendency of a cell to turn to a certain angle without the presence of any obvious external factors. The simulation is able to produce both gliding pattern and spontaneous aggregation center formation as observed in experiments. The model is tested against several known M. xanthus mutants and our modification of parameter values relevant for the individual mutants produces good phenotypic agreements. This outcome indicates the strong predictive potential of our model for the social behaviors of uncharacterized mutants and their expected phenotypes during development
The Geometry of Soft Materials: A Primer
We present an overview of the differential geometry of curves and surfaces
using examples from soft matter as illustrations. The presentation requires a
background only in vector calculus and is otherwise self-contained.Comment: 45 pages, RevTeX, 12 eps figure
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