130 research outputs found
Negative mass corrections in a dissipative stochastic environment
We study the dynamics of a macroscopic object interacting with a dissipative stochastic environment using an adiabatic perturbation theory. The perturbation theory reproduces known expressions for the friction coefficient and, surprisingly, gives an additional negative mass correction. The effect of the negative mass correction is illustrated by studying a harmonic oscillator interacting with a dissipative stochastic environment. While it is well known that the friction coefficient causes a reduction of the oscillation frequency, we show that the negative mass correction can lead to its enhancement. By studying an exactly solvable model of a magnet coupled to a spin environment evolving under standard non-conserving dynamics we show that the effect is present even beyond the validity of the adiabatic perturbation theory.We are grateful to M Kolodrubetz for the careful reading of the manuscript and helpful comments. This work was partially supported by BSF 2010318 (YK and AP), NSF DMR-1506340 (LD and AP), AFOSR FA9550-10-1-0110 (LD and AP), ARO W911NF1410540 (LD and AP) and ISF grant (YK). LD acknowledges the office of Naval Research. YK is grateful to the BU visitors program. (2010318 - BSF; DMR-1506340 - NSF; FA9550-10-1-0110 - AFOSR; W911NF1410540 - ARO; ISF grant)Accepted manuscrip
Chemotaxis When Bacteria Remember: Drift versus Diffusion
{\sl Escherichia coli} ({\sl E. coli}) bacteria govern their trajectories by
switching between running and tumbling modes as a function of the nutrient
concentration they experienced in the past. At short time one observes a drift
of the bacterial population, while at long time one observes accumulation in
high-nutrient regions. Recent work has viewed chemotaxis as a compromise
between drift toward favorable regions and accumulation in favorable regions. A
number of earlier studies assume that a bacterium resets its memory at tumbles
-- a fact not borne out by experiment -- and make use of approximate
coarse-grained descriptions. Here, we revisit the problem of chemotaxis without
resorting to any memory resets. We find that when bacteria respond to the
environment in a non-adaptive manner, chemotaxis is generally dominated by
diffusion, whereas when bacteria respond in an adaptive manner, chemotaxis is
dominated by a bias in the motion. In the adaptive case, favorable drift occurs
together with favorable accumulation. We derive our results from detailed
simulations and a variety of analytical arguments. In particular, we introduce
a new coarse-grained description of chemotaxis as biased diffusion, and we
discuss the way it departs from older coarse-grained descriptions.Comment: Revised version, journal reference adde
Scaling in DNA unzipping models: denaturated loops and end-segments as branches of a block copolymer network
For a model of DNA denaturation, exponents describing the distributions of
denaturated loops and unzipped end-segments are determined by exact enumeration
and by Monte Carlo simulations in two and three dimensions. The loop
distributions are consistent with first order thermal denaturation in both
cases. Results for end-segments show a coexistence of two distinct power laws
in the relative distributions, which is not foreseen by a recent approach in
which DNA is treated as a homogeneous network of linear polymer segments. This
unexpected feature, and the discrepancies with such an approach, are explained
in terms of a refined scaling picture in which a precise distinction is made
between network branches representing single stranded and effective double
stranded segments.Comment: 8 pages, 8 figure
Gene therapy for articular cartilage repair
Articular cartilage serves as the gliding surface of joints. It is susceptible to damage from trauma and from degenerative diseases. Restoration of damaged articular cartilage may be achievable through the use of cell-regulatory molecules that augment the reparative activities of the cells, inhibit the cells\u27; degradative activities, or both. A variety of such molecules have been identified. These include insulin-like growth factor I, fibroblast growth factor 2, bone morphogenetic proteins 2, 4, and 7, and interleukin-1 receptor antagonist. It is now possible to transfer the genes encoding such molecules into articular cartilage and synovial lining cells. Although preliminary, data from in-vitro and in-vivo studies suggest that gene therapy can deliver such potentially therapeutic agents to protect existing cartilage and to build new cartilage.
Keywords: gene therapy, vectors, articular cartilage, arthritis, animal model
Classes of fast and specific search mechanisms for proteins on DNA
Problems of search and recognition appear over different scales in biological
systems. In this review we focus on the challenges posed by interactions
between proteins, in particular transcription factors, and DNA and possible
mechanisms which allow for a fast and selective target location. Initially we
argue that DNA-binding proteins can be classified, broadly, into three distinct
classes which we illustrate using experimental data. Each class calls for a
different search process and we discuss the possible application of different
search mechanisms proposed over the years to each class. The main thrust of
this review is a new mechanism which is based on barrier discrimination. We
introduce the model and analyze in detail its consequences. It is shown that
this mechanism applies to all classes of transcription factors and can lead to
a fast and specific search. Moreover, it is shown that the mechanism has
interesting transient features which allow for stability at the target despite
rapid binding and unbinding of the transcription factor from the target.Comment: 65 pages, 23 figure
Phase Separation and Coarsening in One-Dimensional Driven Diffusive Systems: Local Dynaimcs Leading to Long-Range Hamiltonians
A driven system of three species of particle diffusing on a ring is studied
in detail. The dynamics is local and conserves the three densities. A simple
argument suggesting that the model should phase separate and break the
translational symmetry is given. We show that for the special case where the
three densities are equal the model obeys detailed balance and the steady-state
distribution is governed by a Hamiltonian with asymmetric long-range
interactions. This provides an explicit demonstration of a simple mechanism for
breaking of ergodicity in one dimension. The steady state of finite-size
systems is studied using a generalized matrix product ansatz. The coarsening
process leading to phase separation is studied numerically and in a mean-field
model. The system exhibits slow dynamics due to trapping in metastable states
whose number is exponentially large in the system size. The typical domain size
is shown to grow logarithmically in time. Generalizations to a larger number of
species are discussed.Comment: Revtex, 29 Pages, 7 figures, uses epsf.sty, submitted to Phys. Rev.
Quantum Fluctuation Theorems
Recent advances in experimental techniques allow one to measure and control
systems at the level of single molecules and atoms. Here gaining information
about fluctuating thermodynamic quantities is crucial for understanding
nonequilibrium thermodynamic behavior of small systems. To achieve this aim,
stochastic thermodynamics offers a theoretical framework, and nonequilibrium
equalities such as Jarzynski equality and fluctuation theorems provide key
information about the fluctuating thermodynamic quantities. We review the
recent progress in quantum fluctuation theorems, including the studies of
Maxwell's demon which plays a crucial role in connecting thermodynamics with
information.Comment: As a chapter of: F. Binder, L. A. Correa, C. Gogolin, J. Anders, and
G. Adesso (eds.), "Thermodynamics in the quantum regime - Fundamental Aspects
and New Directions", (Springer International Publishing, 2018
Tightness of slip-linked polymer chains
We study the interplay between entropy and topological constraints for a
polymer chain in which sliding rings (slip-links) enforce pair contacts between
monomers. These slip-links divide a closed ring polymer into a number of
sub-loops which can exchange length between each other. In the ideal chain
limit, we find the joint probability density function for the sizes of segments
within such a slip-linked polymer chain (paraknot). A particular segment is
tight (small in size) or loose (of the order of the overall size of the
paraknot) depending on both the number of slip-links it incorporates and its
competition with other segments. When self-avoiding interactions are included,
scaling arguments can be used to predict the statistics of segment sizes for
certain paraknot configurations.Comment: 10 pages, 6 figures, REVTeX
Applications of Field-Theoretic Renormalization Group Methods to Reaction-Diffusion Problems
We review the application of field-theoretic renormalization group (RG)
methods to the study of fluctuations in reaction-diffusion problems. We first
investigate the physical origin of universality in these systems, before
comparing RG methods to other available analytic techniques, including exact
solutions and Smoluchowski-type approximations. Starting from the microscopic
reaction-diffusion master equation, we then pedagogically detail the mapping to
a field theory for the single-species reaction k A -> l A (l < k). We employ
this particularly simple but non-trivial system to introduce the
field-theoretic RG tools, including the diagrammatic perturbation expansion,
renormalization, and Callan-Symanzik RG flow equation. We demonstrate how these
techniques permit the calculation of universal quantities such as density decay
exponents and amplitudes via perturbative eps = d_c - d expansions with respect
to the upper critical dimension d_c. With these basics established, we then
provide an overview of more sophisticated applications to multiple species
reactions, disorder effects, L'evy flights, persistence problems, and the
influence of spatial boundaries. We also analyze field-theoretic approaches to
nonequilibrium phase transitions separating active from absorbing states. We
focus particularly on the generic directed percolation universality class, as
well as on the most prominent exception to this class: even-offspring branching
and annihilating random walks. Finally, we summarize the state of the field and
present our perspective on outstanding problems for the future.Comment: 10 figures include
Single-molecule experiments in biological physics: methods and applications
I review single-molecule experiments (SME) in biological physics. Recent
technological developments have provided the tools to design and build
scientific instruments of high enough sensitivity and precision to manipulate
and visualize individual molecules and measure microscopic forces. Using SME it
is possible to: manipulate molecules one at a time and measure distributions
describing molecular properties; characterize the kinetics of biomolecular
reactions and; detect molecular intermediates. SME provide the additional
information about thermodynamics and kinetics of biomolecular processes. This
complements information obtained in traditional bulk assays. In SME it is also
possible to measure small energies and detect large Brownian deviations in
biomolecular reactions, thereby offering new methods and systems to scrutinize
the basic foundations of statistical mechanics. This review is written at a
very introductory level emphasizing the importance of SME to scientists
interested in knowing the common playground of ideas and the interdisciplinary
topics accessible by these techniques. The review discusses SME from an
experimental perspective, first exposing the most common experimental
methodologies and later presenting various molecular systems where such
techniques have been applied. I briefly discuss experimental techniques such as
atomic-force microscopy (AFM), laser optical tweezers (LOT), magnetic tweezers
(MT), biomembrane force probe (BFP) and single-molecule fluorescence (SMF). I
then present several applications of SME to the study of nucleic acids (DNA,
RNA and DNA condensation), proteins (protein-protein interactions, protein
folding and molecular motors). Finally, I discuss applications of SME to the
study of the nonequilibrium thermodynamics of small systems and the
experimental verification of fluctuation theorems. I conclude with a discussion
of open questions and future perspectives.Comment: Latex, 60 pages, 12 figures, Topical Review for J. Phys. C (Cond.
Matt
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