Monte Carlo simulation of melting transition on DNA nanocompartment

DNA nanocompartment is a typical DNA-based machine whose function is dependent of molecular collective effect. Fundamental properties of the device have been addressed via electrochemical analysis, fluorescent microscopy, and atomic force microscopy. Interesting and novel phenomena emerged during the switching of the device. We have found that DNAs in this system exhibit a much steep melting transition compared to ones in bulk solution or conventional DNA array. To achieve an understanding to this discrepancy, we introduced DNA-DNA interaction potential to the conventional Ising-like Zimm-Bragg theory and Peyrard-Bishop model of DNA melting. To avoid unrealistic numerical calculation caused by modification of the Peyrard-Bishop nonlinear Hamiltonian with the DNA-DNA interaction, we established coarse-gained Monte Carlo recursion relations by elucidation of five components of energy change during melting transition. The result suggests that DNA-DNA interaction potential accounts for the observed steep transition.Comment: 12 pages, 5 figure

The ethanolamide metabolite of DHA, docosahexaenoylethanolamine, shows immunomodulating effects in mouse peritoneal and RAW264.7 macrophages: evidence for a new link between fish oil and inflammation

Several mechanisms have been proposed for the positive health effects associated with dietary consumption of long-chain n-3 PUFA (n-3 LC-PUFA) including DHA (22 : 6n-3) and EPA (20 : 5n-3). After dietary intake, LC-PUFA are incorporated into membranes and can be converted to their corresponding N-acylethanolamines (NAE). However, little is known on the biological role of these metabolites. In the present study, we tested a series of unsaturated NAE on the lipopolysaccharide (LPS)-induced NO production in RAW264.7 macrophages. Among the compounds tested, docosahexaenoylethanolamine (DHEA), the ethanolamide of DHA, was found to be the most potent inhibitor, inducing a dose-dependent inhibition of NO release. Immune-modulating properties of DHEA were further studied in the same cell line, demonstrating that DHEA significantly suppressed the production of monocyte chemotactic protein-1 (MCP-1), a cytokine playing a pivotal role in chronic inflammation. In LPS-stimulated mouse peritoneal macrophages, DHEA also reduced MCP-1 and NO production. Furthermore, inhibition was also found to take place at a transcriptional level, as gene expression of MCP-1 and inducible NO synthase was inhibited by DHEA. To summarise, in the present study, we showed that DHEA, a DHA-derived NAE metabolite, modulates inflammation by reducing MCP-1 and NO production and expression. These results provide new leads in molecular mechanisms by which DHA can modulate inflammatory processes

Propfan Test Assessment (PTA)

The objectives of the Propfan Test Assessment (PTA) Program were to validate in flight the structural integrity of large-scale propfan blades and to measure noise characteristics of the propfan in both near and far fields. All program objectives were met or exceeded, on schedule and under budget. A Gulfstream Aerospace Corporation GII aircraft was modified to provide a testbed for the 2.74m (9 ft) diameter Hamilton Standard SR-7 propfan which was driven by a 4475 kw (600 shp) turboshaft engine mounted on the left-hand wing of the aircraft. Flight research tests were performed for 20 combinations of speed and altitude within a flight envelope that extended to Mach numbers of 0.85 and altitudes of 12,192m (40,000 ft). Propfan blade stress, near-field noise on aircraft surfaces, and cabin noise were recorded. Primary variables were propfan power and tip speed, and the nacelle tilt angle. Extensive low altitude far-field noise tests were made to measure flyover and sideline noise and the lateral attenuation of noise. In coopertion with the FAA, tests were also made of flyover noise for the aircraft at 6100m (20,000 ft) and 10,668m (35,000 ft). A final series of tests were flown to evaluate an advanced cabin wall noise treatment that was produced under a separate program by NASA-Langley Research Center

A simple model for DNA denaturation

Following Poland and Scheraga, we consider a simplified model for the denaturation transition of DNA. The two strands are modeled as interacting polymer chains. The attractive interactions, which mimic the pairing between the four bases, are reduced to a single short range binding term. Furthermore, base-pair misalignments are forbidden, implying that this binding term exists only for corresponding (same curvilinear abscissae) monomers of the two chains. We take into account the excluded volume repulsion between monomers of the two chains, but neglect intra-chain repulsion. We find that the excluded volume term generates an effective repulsive interaction between the chains, which decays as $1/r^{d-2}$. Due to this long-range repulsion between the chains, the denaturation transition is first order in any dimension, in agreement with previous studies.Comment: 10 page

Phase transition in a non-conserving driven diffusive system

An asymmetric exclusion process comprising positive particles, negative particles and vacancies is introduced. The model is defined on a ring and the dynamics does not conserve the number of particles. We solve the steady state exactly and show that it can exhibit a continuous phase transition in which the density of vacancies decreases to zero. The model has no absorbing state and furnishes an example of a one-dimensional phase transition in a homogeneous non-conserving system which does not belong to the absorbing state universality classes

Theoretical investigation of finite size effects at DNA melting

We investigated how the finiteness of the length of the sequence affects the phase transition that takes place at DNA melting temperature. For this purpose, we modified the Transfer Integral method to adapt it to the calculation of both extensive (partition function, entropy, specific heat, etc) and non-extensive (order parameter and correlation length) thermodynamic quantities of finite sequences with open boundary conditions, and applied the modified procedure to two different dynamical models. We showed that rounding of the transition clearly takes place when the length of the sequence is decreased. We also performed a finite-size scaling analysis of the two models and showed that the singular part of the free energy can indeed be expressed in terms of an homogeneous function. However, both the correlation length and the average separation between paired bases diverge at the melting transition, so that it is no longer clear to which of these two quantities the length of the system should be compared. Moreover, Josephson's identity is satisfied for none of the investigated models, so that the derivation of the characteristic exponents which appear, for example, in the expression of the specific heat, requires some care

The Dynamics of Zeroth-Order Ultrasensitivity: A Critical Phenomenon in Cell Biology

It is well known since the pioneering work of Goldbeter and Koshland [Proc. Natl. Acad. Sci. USA, vol. 78, pp. 6840-6844 (1981)] that cellular phosphorylation- dephosphorylation cycle (PdPC), catalyzed by kinase and phosphatase under saturated condition with zeroth order enzyme kinetics, exhibits ultrasensitivity, sharp transition. We analyse the dynamics aspects of the zeroth order PdPC kinetics and show a critical slowdown akin to the phase transition in condensed matter physics. We demonstrate that an extremely simple, though somewhat mathematically "singular" model is a faithful representation of the ultrasentivity phenomenon. The simplified mathematical model will be valuable, as a component, in developing complex cellular signaling network theory as well as having a pedagogic value.Comment: 8 pages, 3 figure

Why is the DNA Denaturation Transition First Order?

We study a model for the denaturation transition of DNA in which the molecules are considered as composed of a sequence of alternating bound segments and denaturated loops. We take into account the excluded-volume interactions between denaturated loops and the rest of the chain by exploiting recent results on scaling properties of polymer networks of arbitrary topology. The phase transition is found to be first order in d=2 dimensions and above, in agreement with experiments and at variance with previous theoretical results, in which only excluded-volume interactions within denaturated loops were taken into account. Our results agree with recent numerical simulations.Comment: Revised version. To appear in Phys. Rev. Let

DNA sequence from the unzipping force? : one mutation problem

The possibility of detecting mutations in a DNA from force measurements (as a first step towards sequence analysis) is discussed theoretically based on exact calculations. The force signal is associated with the domain wall separating the zipped from the unzipped regions. We propose a comparison method (``differential force microscope'') to detect mutations. Two lattice models are treated as specific examples.Comment: 11 pages, 4 figures. Revised version with minor changes. Paragraph with discussion on experiments added. Accepted for publication in J. Phys. A as a Letter to the Edito