74 research outputs found
Reduced-Order Modeling of Turbulent Reacting Flows with Application to Ramjets and Scramjets
Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/90621/1/AIAA-50272-117.pd
Counterion Penetration and Effective Electrostatic Interactions in Solutions of Polyelectrolyte Stars and Microgels
Counterion distributions and effective electrostatic interactions between
spherical macroions in polyelectrolyte solutions are calculated via
second-order perturbation (linear response) theory. By modelling the macroions
as continuous charge distributions that are permeable to counterions,
analytical expressions are obtained for counterion profiles and effective pair
interactions in solutions of star-branched and microgel macroions. The
counterions are found to penetrate stars more easily than microgels, with
important implications for screening of bare macroion interactions. The
effective pair interactions are Yukawa in form for separated macroions, but are
softly repulsive and bounded for overlapping macroions. A one-body volume
energy, which depends on the average macroion concentration, emerges naturally
in the theory and contributes to the total free energy.Comment: 15 pages, 5 figure
Persistence length of a polyelectrolyte in salty water: a Monte-Carlo study
We address the long standing problem of the dependence of the electrostatic
persistence length of a flexible polyelectrolyte (PE) on the screening
length of the solution within the linear Debye-Huckel theory. The
standard Odijk, Skolnick and Fixman (OSF) theory suggests ,
while some variational theories and computer simulations suggest . In this paper, we use Monte-Carlo simulations to study the conformation
of a simple polyelectrolyte. Using four times longer PEs than in previous
simulations and refined methods for the treatment of the simulation data, we
show that the results are consistent with the OSF dependence . The linear charge density of the PE which enters in the coefficient of
this dependence is properly renormalized to take into account local
fluctuations.Comment: 7 pages, 6 figures. Various corrections in text and reference
Dynamics of Collapse of flexible Polyelectrolytes and Polyampholytes
We provide a theory for the dynamics of collapse of strongly charged
polyelectrolytes (PEs) and flexible polyampholytes (PAs) using Langevin
equation. After the initial stage, in which counterions condense onto PE, the
mechanism of approach to the globular state is similar for PE and PA. In both
instances, metastable pearl-necklace structures form in characteristic time
scale that is proportional to N^{4/5} where N is the number of monomers. The
late stage of collapse occurs by merger of clusters with the largest one
growing at the expense of smaller ones (Lifshitz- Slyozov mechanism). The time
scale for this process T_{COLL} N. Simulations are used to support the proposed
collapse mechanism for PA and PE.Comment: 14 pages, 2 figure
The Persistence Length of a Strongly Charged, Rod-like, Polyelectrolyte in the Presence of Salt
The persistence length of a single, intrinsically rigid polyelectrolyte
chain, above the Manning condensation threshold is investigated theoretically
in presence of added salt. Using a loop expansion method, the partition
function is consistently calculated, taking into account corrections to
mean-field theory. Within a mean-field approximation, the well-known results of
Odijk, Skolnick and Fixman are reproduced. Beyond mean-field, it is found that
density correlations between counterions and thermal fluctuations reduce the
stiffness of the chain, indicating an effective attraction between monomers for
highly charged chains and multivalent counterions. This attraction results in a
possible mechanical instability (collapse), alluding to the phenomenon of DNA
condensation. In addition, we find that more counterions condense on slightly
bent conformations of the chain than predicted by the Manning model for the
case of an infinite cylinder. Finally, our results are compared with previous
models and experiments.Comment: 13 pages, 2 ps figure
A Modified Random Phase Approximation of Polyelectrolyte Solutions
We compute the phase diagram of salt-free polyelectrolyte solutions using a
modified Debye-Huckel Approach. We introduce the chain connectivity via the
Random Phase Approximation with two important modifications. We modify the
electrostatic potential at short distances to include a bound on the
electrostatic attractions at the distance of closest approach between charges.
This modification is shown to act as a hard core in the phase diagram of
electrolyte solutions. We also introduce a cut-off on the integration of the
modes of wave length smaller than the size over which the chains are strongly
perturbed by the electrostatic interactions. This cut-off is shown to be
essential to predict physical phase diagram in long chain solutions
DNA Clasping by Mycobacterial HU: The C-Terminal Region of HupB Mediates Increased Specificity of DNA Binding
BACKGROUND: HU a small, basic, histone like protein is a major component of the bacterial nucleoid. E. coli has two subunits of HU coded by hupA and hupB genes whereas Mycobacterium tuberculosis (Mtb) has only one subunit of HU coded by ORF Rv2986c (hupB gene). One noticeable feature regarding Mtb HupB, based on sequence alignment of HU orthologs from different bacteria, was that HupB(Mtb) bears at its C-terminal end, a highly basic extension and this prompted an examination of its role in Mtb HupB function. METHODOLOGY/PRINCIPAL FINDINGS: With this objective two clones of Mtb HupB were generated; one expressing full length HupB protein (HupB(Mtb)) and another which expresses only the N terminal region (first 95 amino acid) of hupB (HupB(MtbN)). Gel retardation assays revealed that HupB(MtbN) is almost like E. coli HU (heat stable nucleoid protein) in terms of its DNA binding, with a binding constant (K(d)) for linear dsDNA greater than 1000 nM, a value comparable to that obtained for the HUalphaalpha and HUalphabeta forms. However CTR (C-terminal Region) of HupB(Mtb) imparts greater specificity in DNA binding. HupB(Mtb) protein binds more strongly to supercoiled plasmid DNA than to linear DNA, also this binding is very stable as it provides DNase I protection even up to 5 minutes. Similar results were obtained when the abilities of both proteins to mediate protection against DNA strand cleavage by hydroxyl radicals generated by the Fenton's reaction, were compared. It was also observed that both the proteins have DNA binding preference for A:T rich DNA which may occur at the regulatory regions of ORFs and the oriC region of Mtb. CONCLUSIONS/SIGNIFICANCE: These data thus point that HupB(Mtb) may participate in chromosome organization in-vivo, it may also play a passive, possibly an architectural role
Unified Homogenization Theory for Magnetoinductive and Electromagnetic Waves in Split Ring Metamaterials
A unified homogenization procedure for split ring metamaterials taking into
account time and spatial dispersion is introduced. The procedure is based on
two coupled systems of equations. The first one comes from an approximation of
the metamaterial as a cubic arrangement of coupled LC circuits, giving the
relation between currents and local magnetic field. The second equation comes
from macroscopic Maxwell equations, and gives the relation between the
macroscopic magnetic field and the average magnetization of the metamaterial.
It is shown that electromagnetic and magnetoinductive waves propagating in the
metamaterial are obtained from this analysis. Therefore, the proposed time and
spatially dispersive permeability accounts for the characterization of the
complete spectrum of waves of the metamaterial. Finally, it is shown that the
proposed theory is in good quantitative and qualitative agreement with full
wave simulations.Comment: 4 pages, 3 figure
Structure of Metaphase Chromosomes: A Role for Effects of Macromolecular Crowding
In metaphase chromosomes, chromatin is compacted to a concentration of several hundred mg/ml by mechanisms which remain elusive. Effects mediated by the ionic environment are considered most frequently because mono- and di-valent cations cause polynucleosome chains to form compact ∼30-nm diameter fibres in vitro, but this conformation is not detected in chromosomes in situ. A further unconsidered factor is predicted to influence the compaction of chromosomes, namely the forces which arise from crowding by macromolecules in the surrounding cytoplasm whose measured concentration is 100–200 mg/ml. To mimic these conditions, chromosomes were released from mitotic CHO cells in solutions containing an inert volume-occupying macromolecule (8 kDa polyethylene glycol, 10.5 kDa dextran, or 70 kDa Ficoll) in 100 µM K-Hepes buffer, with contaminating cations at only low micromolar concentrations. Optical and electron microscopy showed that these chromosomes conserved their characteristic structure and compaction, and their volume varied inversely with the concentration of a crowding macromolecule. They showed a canonical nucleosomal structure and contained the characteristic proteins topoisomerase IIα and the condensin subunit SMC2. These observations, together with evidence that the cytoplasm is crowded in vivo, suggest that macromolecular crowding effects should be considered a significant and perhaps major factor in compacting chromosomes. This model may explain why ∼30-nm fibres characteristic of cation-mediated compaction are not seen in chromosomes in situ. Considering that crowding by cytoplasmic macromolecules maintains the compaction of bacterial chromosomes and has been proposed to form the liquid crystalline chromosomes of dinoflagellates, a crowded environment may be an essential characteristic of all genomes
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