1,560 research outputs found
Floating-bending tensile-integrity structures
This is a conceptual work about the form-finding of a hybrid tensegrity structure. The structure was obtained from the combination of arch-supported membrane systems and diamond-type tensegrity systems. By combining these two types of structures, the resulting system features the “tensile-integrity” property of cables and membrane together with what we call “floating-bending” of the arches, a term which is intended to recall the words “floating-compression” introduced by Kenneth Snelson, the father of tensegrities. Two approaches in the form-finding calculations were followed, the Matlab implementation of a simple model comprising standard constant-stress membrane/cable elements together with the so-called stick-andspring elements for the arches, and the analysis with the commercial software WinTess, used in conjunction with Rhino and Grasshopper. The case study of a T3 floatingbending tensile-integrity structure was explored, a structure that features a much larger enclosed volume in comparison to conventional tensegrity prisms. The structural design of an outdoor pavilion of 6 m in height was carried out considering ultimate and service limit states. This study shows that floating-bending structures are feasible, opening the way to the introduction of suitable analysis and optimization procedures for this type of structure
A Coarse Grained Model for DNA and Polymer Packaging: Statics and Dynamics
We present a numerical characterization of the statics and dynamics of the packaging of a semi-flexible polymer inside a sphere. The study is motivated by recent experiments on the packaging of DNA inside viral capsids. It is found that the force required to confine the coarse-grained polymer is in fair agreement with that found in experiments for the packaging of the phi29 bacteriophage genome. Despite its schematic nature, the model is capable of reproducing the most salient dynamical features of packaging experiments such as the presence of pauses during individual packaging processes and the trend of the resisting force as a function of chain packed fraction
Role of Secondary Motifs in Fast Folding Polymers: A Dynamical Variational Principle
A fascinating and open question challenging biochemistry, physics and even
geometry is the presence of highly regular motifs such as alpha-helices in the
folded state of biopolymers and proteins. Stimulating explanations ranging from
chemical propensity to simple geometrical reasoning have been invoked to
rationalize the existence of such secondary structures. We formulate a
dynamical variational principle for selection in conformation space based on
the requirement that the backbone of the native state of biologically viable
polymers be rapidly accessible from the denatured state. The variational
principle is shown to result in the emergence of helical order in compact
structures.Comment: 4 pages, RevTex, 4 eps figure
Influence of conformational fluctuations on enzymatic activity: modelling the functional motion of beta-secretase
Considerable insight into the functional activity of proteins and enzymes can
be obtained by studying the low-energy conformational distortions that the
biopolymer can sustain. We carry out the characterization of these large scale
structural changes for a protein of considerable pharmaceutical interest, the
human -secretase. Starting from the crystallographic structure of the
protein, we use the recently introduced beta-Gaussian model to identify, with
negligible computational expenditure, the most significant distortion occurring
in thermal equilibrium and the associated time scales. The application of this
strategy allows to gain considerable insight into the putative functional
movements and, furthermore, helps to identify a handful of key regions in the
protein which have an important mechanical influence on the enzymatic activity
despite being spatially distant from the active site. The results obtained
within the Gaussian model are validated through an extensive comparison against
an all-atom Molecular Dynamics simulation.Comment: To be published in a special issue of J. Phys.: Cond. Mat. (Bedlewo
Workshop
Numerical study of linear and circular model DNA chains confined in a slit: metric and topological properties
Advanced Monte Carlo simulations are used to study the effect of nano-slit
confinement on metric and topological properties of model DNA chains. We
consider both linear and circularised chains with contour lengths in the
1.2--4.8 m range and slits widths spanning continuously the 50--1250nm
range. The metric scaling predicted by de Gennes' blob model is shown to hold
for both linear and circularised DNA up to the strongest levels of confinement.
More notably, the topological properties of the circularised DNA molecules have
two major differences compared to three-dimensional confinement. First, the
overall knotting probability is non-monotonic for increasing confinement and
can be largely enhanced or suppressed compared to the bulk case by simply
varying the slit width. Secondly, the knot population consists of knots that
are far simpler than for three-dimensional confinement. The results suggest
that nano-slits could be used in nano-fluidic setups to produce DNA rings
having simple topologies (including the unknot) or to separate heterogeneous
ensembles of DNA rings by knot type.Comment: 12 pages, 10 figure
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