1,140 research outputs found
Probing molecular free energy landscapes by periodic loading
Single molecule pulling experiments provide information about interactions in
biomolecules that cannot be obtained by any other method. However, the
reconstruction of the molecule's free energy profile from the experimental data
is still a challenge, in particular for the unstable barrier regions. We
propose a new method for obtaining the full profile by introducing a periodic
ramp and using Jarzynski's identity for obtaining equilibrium quantities from
non-equilibrium data. Our simulated experiments show that this method delivers
significant more accurate data than previous methods, under the constraint of
equal experimental effort.Comment: 4 pages, 3 figure
Optical sorting and detection of sub-micron objects in a motional standing wave
An extended interference pattern close to surface may result in both a
transmissive or evanescent surface fields for large area manipulation of
trapped particles. The affinity of differing particle sizes to a moving
standing wave light pattern allows us to hold and deliver them in a
bi-directional manner and importantly demonstrate experimentally particle
sorting in the sub-micron region. This is performed without the need of fluid
flow (static sorting). Theoretical calculations experimentally confirm that
certain sizes of colloidal particles thermally hop more easily between
neighboring traps. A new generic method is also presented for particle position
detection in an extended periodic light pattern and applied to characterization
of optical traps and particle behaviorComment: 5 pages, 6 figures, Optical Trapping pape
Stability of adhesion clusters under constant force
We solve the stochastic equations for a cluster of parallel bonds with shared
constant loading, rebinding and the completely dissociated state as an
absorbing boundary. In the small force regime, cluster lifetime grows only
logarithmically with bond number for weak rebinding, but exponentially for
strong rebinding. Therefore rebinding is essential to ensure physiological
lifetimes. The number of bonds decays exponentially with time for most cases,
but in the intermediate force regime, a small increase in loading can lead to
much faster decay. This effect might be used by cell-matrix adhesions to induce
signaling events through cytoskeletal loading.Comment: Revtex, 4 pages, 4 Postscript files include
On Iterated Twisted Tensor Products of Algebras
We introduce and study the definition, main properties and applications of
iterated twisted tensor products of algebras, motivated by the problem of
defining a suitable representative for the product of spaces in noncommutative
geometry. We find conditions for constructing an iterated product of three
factors, and prove that they are enough for building an iterated product of any
number of factors. As an example of the geometrical aspects of our
construction, we show how to construct differential forms and involutions on
iterated products starting from the corresponding structures on the factors,
and give some examples of algebras that can be described within our theory. We
prove a certain result (called ``invariance under twisting'') for a twisted
tensor product of two algebras, stating that the twisted tensor product does
not change when we apply certain kind of deformation. Under certain conditions,
this invariance can be iterated, containing as particular cases a number of
independent and previously unrelated results from Hopf algebra theory.Comment: 44 pages, 21 figures. More minor typos corrections, one more example
and some references adde
Escape from a metastable well under a time-ramped force
Thermally activated escape of an over-damped particle from a metastable well
under the action of a time-ramped force is studied. We express the mean first
passage time (MFPT) as the solution to a partial differential equation, which
we solve numerically for a model case. We discuss two approximations of the
MFPT, one of which works remarkably well over a wide range of loading rates,
while the second is easy to calculate and can provide a valuable first
estimate.Comment: 9 pages, including 2 figure
Small Universal Accepting Networks of Evolutionary Processors with Filtered Connections
In this paper, we present some results regarding the size complexity of
Accepting Networks of Evolutionary Processors with Filtered Connections
(ANEPFCs). We show that there are universal ANEPFCs of size 10, by devising a
method for simulating 2-Tag Systems. This result significantly improves the
known upper bound for the size of universal ANEPFCs which is 18.
We also propose a new, computationally and descriptionally efficient
simulation of nondeterministic Turing machines by ANEPFCs. More precisely, we
describe (informally, due to space limitations) how ANEPFCs with 16 nodes can
simulate in O(f(n)) time any nondeterministic Turing machine of time complexity
f(n). Thus the known upper bound for the number of nodes in a network
simulating an arbitrary Turing machine is decreased from 26 to 16
Rupture of multiple parallel molecular bonds under dynamic loading
Biological adhesion often involves several pairs of specific receptor-ligand
molecules. Using rate equations, we study theoretically the rupture of such
multiple parallel bonds under dynamic loading assisted by thermal activation.
For a simple generic type of cooperativity, both the rupture time and force
exhibit several different scaling regimes. The dependence of the rupture force
on the number of bonds is predicted to be either linear, like a square root or
logarithmic.Comment: 8 pages, 2 figure
Elastic properties of grafted microtubules
We use single-particle tracking to study the elastic properties of single
microtubules grafted to a substrate. Thermal fluctuations of the free
microtubule's end are recorded, in order to measure position distribution
functions from which we calculate the persistence length of microtubules with
contour lengths between 2.6 and 48 micrometers. We find the persistence length
to vary by more than a factor of 20 over the total range of contour lengths.
Our results support the hypothesis that shearing between protofilaments
contributes significantly to the mechanics of microtubules.Comment: 9 pages, 3 figure
The Kepler Problem with Anisotropic Perturbations
We study a 2-body problem given by the sum of the Newtonian potential and an
anisotropic perturbation that is a homogeneous function of degree ,
. For , the sets of initial conditions leading to
collisions/ejections and the one leading to escapes/captures have positive
measure. For and , the flow on the zero-energy manifold
is chaotic. For , a case we prove integrable, the infinity manifold of
the zero-energy level is a disconnected set, which has heteroclinic connections
with the collision manifold
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