2,255 research outputs found
Compressive force generation by a bundle of living biofilaments
To study the compressional forces exerted by a bundle of living stiff
filaments pressing on a surface, akin to the case of an actin bundle in
filopodia structures, we have performed particulate Molecular Dynamics
simulations of a grafted bundle of parallel living (self-assembling) filaments,
in chemical equilibrium with a solution of their constitutive monomers.
Equilibrium is established as these filaments, grafted at one end to a wall of
the simulation box, grow at their chemically active free end and encounter the
opposite confining wall of the simulation box. Further growth of filaments
requires bending and thus energy, which automatically limit the populations of
longer filaments. The resulting filament sizes distribution and the force
exerted by the bundle on the obstacle are analyzed for different grafting
densities and different sub- or supercritical conditions, these properties
being compared with the predictions of the corresponding ideal confined bundle
model. In this analysis, non-ideal effects due to interactions between
filaments and confinement effects are singled out. For all state points
considered at the same temperature and at the same gap width between the two
surfaces, the force per filament exerted on the opposite wall appears to be a
function of a rescaled free monomer density . This
quantity can be estimated directly from the characteristic length of the
exponential filament size distribution observed in the size domain where
these grafted filaments are not in direct contact with the wall. We also
analyze the dynamics of the filament contour length fluctuations in terms of
effective polymerization () and depolymerization () rates, where again it
is possible to disentangle non-ideal and confinement effects.Comment: 24 pages, 7 figure
On the Properties of a Bundle of Flexible Actin Filaments in an Optical Trap
We establish the Statistical Mechanics framework for a bundle of Nf living
and uncrosslinked actin filaments in a supercritical solution of free monomers
pressing against a mobile wall. The filaments are anchored normally to a fixed
planar surface at one of their ends and, because of their limited flexibility,
they grow almost parallel to each other. Their growing ends hit a moving
obstacle, depicted as a second planar wall, parallel to the previous one and
subjected to a harmonic compressive force. The force constant is denoted as
trap strength while the distance between the two walls as trap length to make
contact with the experimental optical trap apparatus. For an ideal solution of
reactive filaments and free monomers at fixed free monomers chemical potential,
we obtain the general expression for the grand potential from which we derive
averages and distributions of relevant physical quantities, namely the obstacle
position, the bundle polymerization force and the number of filaments in direct
contact with the wall. The grafted living filaments are modeled as discrete
Wormlike chains, with Factin persistence length, subject to discrete contour
length variations to model single monomer (de)polymerization steps. Rigid
filaments, either isolated or in bundles, all provide average values of the
stalling force in agreement with Hill's predictions, independent of the average
trap length. Flexible filaments instead, for values of the trap strength
suitable to prevent their lateral escape, provide an average bundle force and
an average trap length slightly larger than the corresponding rigid cases (few
percents). Still the stalling force remains nearly independent on the average
trap length, but results from the product of two strongly L dependent
contributions: the fraction of touching filaments and the single filament
buckling force.Comment: 21 pages, 8 figure
When Both Transmitting and Receiving Energies Matter: An Application of Network Coding in Wireless Body Area Networks
A network coding scheme for practical implementations of wireless body area
networks is presented, with the objective of providing reliability under
low-energy constraints. We propose a simple network layer protocol for star
networks, adapting redundancy based on both transmission and reception energies
for data and control packets, as well as channel conditions. Our numerical
results show that even for small networks, the amount of energy reduction
achievable can range from 29% to 87%, as the receiving energy per control
packet increases from equal to much larger than the transmitting energy per
data packet. The achievable gains increase as a) more nodes are added to the
network, and/or b) the channels seen by different sensor nodes become more
asymmetric.Comment: 10 pages, 7 figures, submitted to the NC-Pro Workshop at IFIP
Networking Conference 2011, and to appear in the conference proceedings,
published by Springer-Verlag, in the Lecture Notes in Computer Science (LNCS)
serie
Low-power, low-penalty, flip-chip integrated, 10Gb/s ring-based 1V CMOS photonics transmitter
Modulation with 7.5dB transmitter penalty is demonstrated from a novel 1.5Vpp differential CMOS driver flip-chip integrated with a Si ring modulator, consuming 350fJ/bit from a single 1V supply at bit rates up to 10Gb/s
A Fully Differential Digital CMOS Pulse UWB Generator
A new fully-digital CMOS pulse generator for impulse-radio Ultra-Wide-Band (UWB) systems is presented. First, the shape of the pulse which best fits the FCC regulation in the 3.1-5 GHz sub-band of the entire 3.1-10.6 GHz UWB bandwidth is derived and approximated using rectangular digital pulses. In particular, the number and width of pulses that approximate an ideal template is found through an ad-hoc optimization methodology. Then a fully differential digital CMOS circuit that synthesizes the pulse sequence is conceived and its functionality demonstrated through post-layout simulations. The results show a very good agreement with the FCC requirements and a low power consumptio
Geometric Generalisations of SHAKE and RATTLE
A geometric analysis of the Shake and Rattle methods for constrained
Hamiltonian problems is carried out. The study reveals the underlying
differential geometric foundation of the two methods, and the exact relation
between them. In addition, the geometric insight naturally generalises Shake
and Rattle to allow for a strictly larger class of constrained Hamiltonian
systems than in the classical setting.
In order for Shake and Rattle to be well defined, two basic assumptions are
needed. First, a nondegeneracy assumption, which is a condition on the
Hamiltonian, i.e., on the dynamics of the system. Second, a coisotropy
assumption, which is a condition on the geometry of the constrained phase
space. Non-trivial examples of systems fulfilling, and failing to fulfill,
these assumptions are given
Molecular dynamics simulation of polymer helix formation using rigid-link methods
Molecular dynamics simulations are used to study structure formation in
simple model polymer chains that are subject to excluded volume and torsional
interactions. The changing conformations exhibited by chains of different
lengths under gradual cooling are followed until each reaches a state from
which no further change is possible. The interactions are chosen so that the
true ground state is a helix, and a high proportion of simulation runs succeed
in reaching this state; the fraction that manage to form defect-free helices is
a function of both chain length and cooling rate. In order to demonstrate
behavior analogous to the formation of protein tertiary structure, additional
attractive interactions are introduced into the model, leading to the
appearance of aligned, antiparallel helix pairs. The simulations employ a
computational approach that deals directly with the internal coordinates in a
recursive manner; this representation is able to maintain constant bond lengths
and angles without the necessity of treating them as an algebraic constraint
problem supplementary to the equations of motion.Comment: 15 pages, 14 figure
Recurrence quantification analysis as a tool for the characterization of molecular dynamics simulations
A molecular dynamics simulation of a Lennard-Jones fluid, and a trajectory of
the B1 immunoglobulin G-binding domain of streptococcal protein G (B1-IgG)
simulated in water are analyzed by recurrence quantification, which is
noteworthy for its independence from stationarity constraints, as well as its
ability to detect transients, and both linear and nonlinear state changes. The
results demonstrate the sensitivity of the technique for the discrimination of
phase sensitive dynamics. Physical interpretation of the recurrence measures is
also discussed.Comment: 7 pages, 8 figures, revtex; revised for review for Phys. Rev. E
(clarifications and expansion of discussion)-- addition of the 8 postscript
figures previously omitted, but unchanged from version
Maximum Flux Transition Paths of Conformational Change
Given two metastable states A and B of a biomolecular system, the problem is
to calculate the likely paths of the transition from A to B. Such a calculation
is more informative and more manageable if done for a reduced set of collective
variables chosen so that paths cluster in collective variable space. The
computational task becomes that of computing the "center" of such a cluster. A
good way to define the center employs the concept of a committor, whose value
at a point in collective variable space is the probability that a trajectory at
that point will reach B before A. The committor "foliates" the transition
region into a set of isocommittors. The maximum flux transition path is defined
as a path that crosses each isocommittor at a point which (locally) has the
highest crossing rate of distinct reactive trajectories. (This path is
different from that of the MaxFlux method of Huo and Straub.) It is argued that
such a path is nearer to an ideal path than others that have been proposed with
the possible exception of the finite-temperature string method path. To make
the calculation tractable, three approximations are introduced, yielding a path
that is the solution of a nonsingular two-point boundary-value problem. For
such a problem, one can construct a simple and robust algorithm. One such
algorithm and its performance is discussed.Comment: 7 figure
Integrity of H1 helix in prion protein revealed by molecular dynamic simulations to be especially vulnerable to changes in the relative orientation of H1 and its S1 flank
In the template-assistance model, normal prion protein (PrPC), the pathogenic
cause of prion diseases such as Creutzfeldt-Jakob (CJD) in human, Bovine
Spongiform Encephalopathy (BSE) in cow, and scrapie in sheep, converts to
infectious prion (PrPSc) through an autocatalytic process triggered by a
transient interaction between PrPC and PrPSc. Conventional studies suggest the
S1-H1-S2 region in PrPC to be the template of S1-S2 -sheet in PrPSc, and
the conformational conversion of PrPC into PrPSc may involve an unfolding of H1
in PrPC and its refolding into the -sheet in PrPSc. Here we conduct a
series of simulation experiments to test the idea of transient interaction of
the template-assistance model. We find that the integrity of H1 in PrPC is
vulnerable to a transient interaction that alters the native dihedral angles at
residue Asn, which connects the S1 flank to H1, but not to interactions
that alter the internal structure of the S1 flank, nor to those that alter the
relative orientation between H1 and the S2 flank.Comment: A major revision on statistical analysis method has been made. The
paper now has 23 pages, 11 figures. This work was presented at 2006 APS March
meeting session K29.0004 at Baltimore, MD, USA 3/13-17, 2006. This paper has
been accepted for pubcliation in European Biophysical Journal on Feb 2, 200
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