1,270 research outputs found
Multistability of free spontaneously-curved anisotropic strips
Multistable structures are objects with more than one stable conformation,
exemplified by the simple switch. Continuum versions are often elastic
composite plates or shells, such as the common measuring tape or the slap
bracelet, both of which exhibit two stable configurations: rolled and unrolled.
Here we consider the energy landscape of a general class of multistable
anisotropic strips with spontaneous Gaussian curvature. We show that while
strips with non-zero Gaussian curvature can be bistable, strips with positive
spontaneous curvature are always bistable, independent of the elastic moduli,
strips of spontaneous negative curvature are bistable only in the presence of
spontaneous twist and when certain conditions on the relative stiffness of the
strip in tension and shear are satisfied. Furthermore, anisotropic strips can
become tristable when their bending rigidity is small. Our study complements
and extends the theory of multistability in anisotropic shells and suggests new
design criteria for these structures.Comment: 20 pages, 10 figure
Statics and Dynamics of the Wormlike Bundle Model
Bundles of filamentous polymers are primary structural components of a broad
range of cytoskeletal structures, and their mechanical properties play key
roles in cellular functions ranging from locomotion to mechanotransduction and
fertilization. We give a detailed derivation of a wormlike bundle model as a
generic description for the statics and dynamics of polymer bundles consisting
of semiflexible polymers interconnected by crosslinking agents. The elastic
degrees of freedom include bending as well as twist deformations of the
filaments and shear deformation of the crosslinks. We show that a competition
between the elastic properties of the filaments and those of the crosslinks
leads to renormalized effective bend and twist rigidities that become
mode-number dependent. The strength and character of this dependence is found
to vary with bundle architecture, such as the arrangement of filaments in the
cross section and pretwist. We discuss two paradigmatic cases of bundle
architecture, a uniform arrangement of filaments as found in F-actin bundles
and a shell-like architecture as characteristic for microtubules. Each
architecture is found to have its own universal ratio of maximal to minimal
bending rigidity, independent of the specific type of crosslink induced
filament coupling; our predictions are in reasonable agreement with available
experimental data for microtubules. Moreover, we analyze the predictions of the
wormlike bundle model for experimental observables such as the tangent-tangent
correlation function and dynamic response and correlation functions. Finally,
we analyze the effect of pretwist (helicity) on the mechanical properties of
bundles. We predict that microtubules with different number of protofilaments
should have distinct variations in their effective bending rigidity
Bubble generation in a twisted and bent DNA-like model
The DNA molecule is modeled by a parabola embedded chain with long-range
interactions between twisted base pair dipoles. A mechanism for bubble
generation is presented and investigated in two different configurations. Using
random normally distributed initial conditions to simulate thermal
fluctuations, a relationship between bubble generation, twist and curvature is
established. An analytical approach supports the numerical results.Comment: 7 pages, 8 figures. Accepted for Phys. Rev. E (in press
Spectral Analysis of Guanine and Cytosine Fluctuations of Mouse Genomic DNA
We study global fluctuations of the guanine and cytosine base content (GC%)
in mouse genomic DNA using spectral analyses. Power spectra S(f) of GC%
fluctuations in all nineteen autosomal and two sex chromosomes are observed to
have the universal functional form S(f) \sim 1/f^alpha (alpha \approx 1) over
several orders of magnitude in the frequency range 10^-7< f < 10^-5 cycle/base,
corresponding to long-ranging GC% correlations at distances between 100 kb and
10 Mb. S(f) for higher frequencies (f > 10^-5 cycle/base) shows a flattened
power-law function with alpha < 1 across all twenty-one chromosomes. The
substitution of about 38% interspersed repeats does not affect the functional
form of S(f), indicating that these are not predominantly responsible for the
long-ranged multi-scale GC% fluctuations in mammalian genomes. Several
biological implications of the large-scale GC% fluctuation are discussed,
including neutral evolutionary history by DNA duplication, chromosomal bands,
spatial distribution of transcription units (genes), replication timing, and
recombination hot spots.Comment: 15 pages (figures included), 2 figure
Large-scale Oscillation of Structure-Related DNA Sequence Features in Human Chromosome 21
Human chromosome 21 is the only chromosome in human genome that exhibits
oscillation of (G+C)-content of cycle length of hundreds kilobases (500 kb near
the right telomere). We aim at establishing the existence of similar
periodicity in structure-related sequence features in order to relate this
(G+C)% oscillation to other biological phenomena. The following quantities are
shown to oscillate with the same 500kb periodicity in human chromosome 21:
binding energy calculated by two sets of dinucleotide-based thermodynamic
parameters, AA/TT and AAA/TTT bi-/tri-nucleotide density, 5'-TA-3' dinucleotide
density, and signal for 10/11-base periodicity of AA/TT or AAA/TTT. These
intrinsic quantities are related to structural features of the double helix of
DNA molecules, such as base-pair binding, untwisting/unwinding, stiffness, and
a putative tendency for nucleosome formation.Comment: submitted to Physical Review
Statistical Mechanics of Torque Induced Denaturation of DNA
A unifying theory of the denaturation transition of DNA, driven by
temperature T or induced by an external mechanical torque Gamma is presented.
Our model couples the hydrogen-bond opening and the untwisting of the
helicoidal molecular structure. We show that denaturation corresponds to a
first-order phase transition from B-DNA to d-DNA phases and that the
coexistence region is naturally parametrized by the degree of supercoiling
sigma. The denaturation free energy, the temperature dependence of the twist
angle, the phase diagram in the T,Gamma plane and isotherms in the sigma, Gamma
plane are calculated and show a good agreement with experimental data.Comment: 5 pages, 3 figures, model improve
Hacia una pedagogía como teoría crítica en la formación de profesores en Ciencias de la Educación
El presente trabajo parte de la siguiente pregunta: ¿Qué lugar ocupa hoy y cuál debería ocupar la Pedagogía en la formación de profesores en Ciencias de la Educación?; y en la búsqueda de una respuesta a esta pregunta surge a posteriori: ¿Se puede pensar la pedagogía como teoría crítica frente a las ciencias de la educación (entendidas como ciencias que producen “Teoría Tradicional”)? Porque si esto fuera así los pedagogos tendríamos la responsabilidad de pensar una teoría de la educación de carácter emancipatorio para poder replantear la cuestión de “¿Hacia dónde va la educación?” Es decir, si la pedagogía es un saber y una reflexión sobre la práctica, debemos poder producir un saber que sea emancipatorio y propositivo que nos permita decir como apuntar al objetivo de la igualdad en la escuela. Es fundamental replantear en la formación de profesionales de la educación ¿Qué es lo que hacemos como educadores?, ¿Qué sentido tiene nuestro trabajo docente? ¿Para qué educar hoy? Habría que repensar el rol de la pedagogía posicionándola como teoría crítica en la formación de profesores en Ciencias de la Educación, teniendo en cuenta este marco actual que se nos presenta.Facultad de Humanidades y Ciencias de la Educació
Calculating singlet excited states: comparison with fast time-resolved infrared spectroscopy of coumarins
In contrast to the ground state, the calculation of the infrared (IR) spectroscopy of molecular singlet excited states represents a substantial challenge. Here we use the structural IR fingerprint of the singlet excited states of a range of coumarin dyes to assess the accuracy of density functional theory based methods for the calculation of excited state IR spectroscopy. It is shown that excited state Kohn-Sham density functional theory provides a high level of accuracy and represents an alternative approach to time-dependent density functional theory for simulating the IR spectroscopy of the singlet excited states
Solitons in Yakushevich-like models of DNA dynamics with improved intrapair potential
The Yakushevich (Y) model provides a very simple pictures of DNA torsion
dynamics, yet yields remarkably correct predictions on certain physical
characteristics of the dynamics. In the standard Y model, the interaction
between bases of a pair is modelled by a harmonic potential, which becomes
anharmonic when described in terms of the rotation angles; here we substitute
to this different types of improved potentials, providing a more physical
description of the H-bond mediated interactions between the bases. We focus in
particular on soliton solutions; the Y model predicts the correct size of the
nonlinear excitations supposed to model the ``transcription bubbles'', and this
is essentially unchanged with the improved potential. Other features of soliton
dynamics, in particular curvature of soliton field configurations and the
Peierls-Nabarro barrier, are instead significantly changed
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