22,042 research outputs found
Twist versus Nonlinear Stacking in Short DNA Molecules
The denaturation of the double helix is a template for fundamental biological
functions such as replication and transcription involving the formation of
local fluctuational openings. The denaturation transition is studied for
heterogeneous short sequences of DNA, i.e. base pairs, in the
framework of a mesoscopic Hamiltonian model which accounts for the helicoidal
geometry of the molecule. The theoretical background for the application of the
path integral formalism to predictive analysis of the molecule thermodynamical
properties is discussed. The base pair displacements with respect to the ground
state are treated as paths whose temperature dependent amplitudes are governed
by the thermal wavelength. The ensemble of base pairs paths is selected, at any
temperature, consistently with both the model potential and the second law of
thermodynamics. The partition function incorporates the effects of the base
pair thermal fluctuations which become stronger close to the denaturation. The
transition appears as a gradual phenomenon starting from the molecule segments
rich in adenine-thymine base pairs. Computing the equilibrium thermodynamics,
we focus on the interplay between twisting of the complementary strands around
the molecule axis and nonlinear stacking potential: it is shown that the latter
affects the melting profiles only if the rotational degrees of freedom are
included in the Hamiltonian. The use of ladder Hamiltonian models for the DNA
complementary strands in the pre-melting regime is questioned.Comment: Journal of Theoretical Biology (2014
Path Integral Method for DNA Denaturation
The statistical physics of homogeneous DNA is investigated by the imaginary
time path integral formalism. The base pair stretchings are described by an
ensemble of paths selected through a macroscopic constraint, the fulfillement
of the second law of thermodynamics. The number of paths contributing to the
partition function strongly increases around and above a specific temperature
whereas the fraction of unbound base pairs grows continuosly around and
above . The latter is identified with the denaturation temperature.
Thus, the separation of the two complementary strands appears as a highly
cooperative phenomenon displaying a smooth crossover versus . The
thermodynamical properties have been computed in a large temperature range by
varying the size of the path ensemble at the lower bound of the range. No
significant physical dependence on the system size has been envisaged. The
entropy grows continuosly versus while the specific heat displays a
remarkable peak at . The location of the peak versus varies with the
stiffness of the anharmonic stacking interaction along the strand. The
presented results suggest that denaturation in homogeneous DNA has the features
of a second order phase transition. The method accounts for the cooperative
behavior of a very large number of degrees of freedom while the computation
time is kept within a reasonable limit.Comment: Physical Review E 2009 in pres
Thermodynamics of Twisted DNA with Solvent Interaction
The imaginary time path integral formalism is applied to a nonlinear
Hamiltonian for a short fragment of heterogeneous DNA with a stabilizing
solvent interaction term. Torsional effects are modeled by a twist angle
between neighboring base pairs stacked along the molecule backbone. The base
pair displacements are described by an ensemble of temperature dependent paths
thus incorporating those fluctuational effects which shape the multisteps
thermal denaturation. By summing over base pair paths, a
large number of double helix configurations is taken into account consistently
with the physical requirements of the model potential. The partition function
is computed as a function of the twist. It is found that the equilibrium twist
angle, peculiar of B-DNA at room temperature, yields the stablest helicoidal
geometry against thermal disruption of the base pair hydrogen bonds. This
result is corroborated by the computation of thermodynamical properties such as
fractions of open base pairs and specific heat.Comment: The Journal of Chemical Physics (2011) in pres
A Comparative Analysis of Ensemble Classifiers: Case Studies in Genomics
The combination of multiple classifiers using ensemble methods is
increasingly important for making progress in a variety of difficult prediction
problems. We present a comparative analysis of several ensemble methods through
two case studies in genomics, namely the prediction of genetic interactions and
protein functions, to demonstrate their efficacy on real-world datasets and
draw useful conclusions about their behavior. These methods include simple
aggregation, meta-learning, cluster-based meta-learning, and ensemble selection
using heterogeneous classifiers trained on resampled data to improve the
diversity of their predictions. We present a detailed analysis of these methods
across 4 genomics datasets and find the best of these methods offer
statistically significant improvements over the state of the art in their
respective domains. In addition, we establish a novel connection between
ensemble selection and meta-learning, demonstrating how both of these disparate
methods establish a balance between ensemble diversity and performance.Comment: 10 pages, 3 figures, 8 tables, to appear in Proceedings of the 2013
International Conference on Data Minin
Phason elasticity of a three-dimensional quasicrystal: transfer-matrix method
We introduce a new transfer matrix method for calculating the thermodynamic
properties of random-tiling models of quasicrystals in any number of
dimensions, and describe how it may be used to calculate the phason elastic
properties of these models, which are related to experimental measurables such
as phason Debye-Waller factors, and diffuse scattering wings near Bragg peaks.
We apply our method to the canonical-cell model of the icosahedral phase,
making use of results from a previously-presented calculation in which the
possible structures for this model under specific periodic boundary conditions
were cataloged using a computational technique. We give results for the
configurational entropy density and the two fundamental elastic constants for a
range of system sizes. The method is general enough allow a similar calculation
to be performed for any other random tiling model.Comment: 38 pages, 3 PostScript figures, self-expanding uuencoded compressed
tar file, LaTeX using RevTeX macros and epsfig.st
Tree-based Intelligent Intrusion Detection System in Internet of Vehicles
The use of autonomous vehicles (AVs) is a promising technology in Intelligent
Transportation Systems (ITSs) to improve safety and driving efficiency.
Vehicle-to-everything (V2X) technology enables communication among vehicles and
other infrastructures. However, AVs and Internet of Vehicles (IoV) are
vulnerable to different types of cyber-attacks such as denial of service,
spoofing, and sniffing attacks. In this paper, an intelligent intrusion
detection system (IDS) is proposed based on tree-structure machine learning
models. The results from the implementation of the proposed intrusion detection
system on standard data sets indicate that the system has the ability to
identify various cyber-attacks in the AV networks. Furthermore, the proposed
ensemble learning and feature selection approaches enable the proposed system
to achieve high detection rate and low computational cost simultaneously.Comment: Accepted in IEEE Global Communications Conference (GLOBECOM) 201
Computing the Absolute Gibbs Free Energy in Atomistic Simulations: Applications to Defects in Solids
The Gibbs free energy is the fundamental thermodynamic potential underlying
the relative stability of different states of matter under constant-pressure
conditions. However, computing this quantity from atomic-scale simulations is
far from trivial. As a consequence, all too often the potential energy of the
system is used as a proxy, overlooking entropic and anharmonic effects. Here we
discuss a combination of different thermodynamic integration routes to obtain
the absolute Gibbs free energy of a solid system starting from a harmonic
reference state. This approach enables the direct comparison between the free
energy of different structures, circumventing the need to sample the transition
paths between them. We showcase this thermodynamic integration scheme by
computing the Gibbs free energy associated with a vacancy in BCC iron, and the
intrinsic stacking fault free energy of nickel. These examples highlight the
pitfalls of estimating the free energy of crystallographic defects only using
the minimum potential energy, which overestimates the vacancy free energy by
60% and the stacking-fault energy by almost 300% at temperatures close to the
melting point
- …