3,010 research outputs found
The Boltzmann factor, DNA melting, and Brownian ratchets: Topics in an introductory physics sequence for biology and premedical students
Three, interrelated biologically-relevant examples of biased random walks are
presented: (1) A model for DNA melting, modelled as DNA unzipping, which
provides a way to illustrate the role of the Boltzmann factor in a venue
well-known to biology and pre-medical students; (2) the activity of helicase
motor proteins in unzipping double-stranded DNA, for example, at the
replication fork, which is an example of a Brownian ratchet; (3) force
generation by actin polymerization, which is another Brownian ratchet, and for
which the force and actin-concentration dependence of the velocity of actin
polymerization is determined
Blinking statistics of a molecular beacon triggered by end-denaturation of DNA
We use a master equation approach based on the Poland-Scheraga free energy
for DNA denaturation to investigate the (un)zipping dynamics of a denaturation
wedge in a stretch of DNA, that is clamped at one end. In particular, we
quantify the blinking dynamics of a fluorophore-quencher pair mounted within
the denaturation wedge. We also study the behavioural changes in the presence
of proteins, that selectively bind to single-stranded DNA. We show that such a
setup could be well-suited as an easy-to-implement nanodevice for sensing
environmental conditions in small volumes.Comment: 14 pages, 5 figures, LaTeX, IOP style. Accepted to J Phys Cond Mat
special issue on diffusio
Breathing dynamics in heteropolymer DNA
While the statistical mechanical description of DNA has a long tradition,
renewed interest in DNA melting from a physics perspective is nourished by
measurements of the fluctuation dynamics of local denaturation bubbles by
single molecule spectroscopy. The dynamical opening of DNA bubbles (DNA
breathing) is supposedly crucial for biological functioning during, for
instance, transcription initiation and DNA's interaction with selectively
single-stranded DNA binding proteins. Motivated by this, we consider the bubble
breathing dynamics in a heteropolymer DNA based on a (2+1)-variable master
equation and complementary stochastic Gillespie simulations, providing the
bubble size and the position of the bubble along the sequence as a function of
time. We utilize new experimental data that independently obtain stacking and
hydrogen bonding contributions to DNA stability. We calculate the spectrum of
relaxation times and the experimentally measurable autocorrelation function of
a fluorophore-quencher tagged base-pair, and demonstrate good agreement with
fluorescence correlation experiments. A significant dependence of opening
probability and waiting time between bubble events on the local DNA sequence is
revealed and quantified for a promoter sequence of the T7 phage. The strong
dependence on sequence, temperature and salt concentration for the breathing
dynamics of DNA found here points at a good potential for nanosensing
applications by utilizing short fluorophore-quencher dressed DNA constructs.Comment: 11 pages, 8 figure
Master equation approach to DNA-breathing in heteropolymer DNA
After crossing an initial barrier to break the first base-pair (bp) in
double-stranded DNA, the disruption of further bps is characterized by free
energies between less than one to a few kT. This causes the opening of
intermittent single-stranded bubbles. Their unzipping and zipping dynamics can
be monitored by single molecule fluorescence or NMR methods. We here establish
a dynamic description of this DNA-breathing in a heteropolymer DNA in terms of
a master equation that governs the time evolution of the joint probability
distribution for the bubble size and position along the sequence. The transfer
coefficients are based on the Poland-Scheraga free energy model. We derive the
autocorrelation function for the bubble dynamics and the associated relaxation
time spectrum. In particular, we show how one can obtain the probability
densities of individual bubble lifetimes and of the waiting times between
successive bubble events from the master equation. A comparison to results of a
stochastic Gillespie simulation shows excellent agreement.Comment: 12 pages, 8 figure
Artificial Sequences and Complexity Measures
In this paper we exploit concepts of information theory to address the
fundamental problem of identifying and defining the most suitable tools to
extract, in a automatic and agnostic way, information from a generic string of
characters. We introduce in particular a class of methods which use in a
crucial way data compression techniques in order to define a measure of
remoteness and distance between pairs of sequences of characters (e.g. texts)
based on their relative information content. We also discuss in detail how
specific features of data compression techniques could be used to introduce the
notion of dictionary of a given sequence and of Artificial Text and we show how
these new tools can be used for information extraction purposes. We point out
the versatility and generality of our method that applies to any kind of
corpora of character strings independently of the type of coding behind them.
We consider as a case study linguistic motivated problems and we present
results for automatic language recognition, authorship attribution and self
consistent-classification.Comment: Revised version, with major changes, of previous "Data Compression
approach to Information Extraction and Classification" by A. Baronchelli and
V. Loreto. 15 pages; 5 figure
Measuring complexity with zippers
Physics concepts have often been borrowed and independently developed by
other fields of science. In this perspective a significant example is that of
entropy in Information Theory. The aim of this paper is to provide a short and
pedagogical introduction to the use of data compression techniques for the
estimate of entropy and other relevant quantities in Information Theory and
Algorithmic Information Theory. We consider in particular the LZ77 algorithm as
case study and discuss how a zipper can be used for information extraction.Comment: 10 pages, 3 figure
Helicase activity on DNA as a propagating front
We develop a propagating front analysis, in terms of a local probability of
zipping, for the helicase activity of opening up a double stranded DNA (dsDNA).
In a fixed-distance ensemble (conjugate to the fixed-force ensemble) the front
separates the zipped and unzipped phases of a dsDNA and a drive acts locally
around the front. Bounds from variational analysis and numerical estimates for
the speed of a helicase are obtained. Different types of helicase behaviours
can be distinguished by the nature of the drive.Comment: 5 pages, 5 eps figures; replaced by the published versio
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