567 research outputs found
Confinement and Viscoelastic effects on Chain Closure Dynamics
Chemical reactions inside cells are typically subject to the effects both of
the cell's confining surfaces and of the viscoelastic behavior of its contents.
In this paper, we show how the outcome of one particular reaction of relevance
to cellular biochemistry - the diffusion-limited cyclization of long chain
polymers - is influenced by such confinement and crowding effects. More
specifically, starting from the Rouse model of polymer dynamics, and invoking
the Wilemski-Fixman approximation, we determine the scaling relationship
between the mean closure time t_{c} of a flexible chain (no excluded volume or
hydrodynamic interactions) and the length N of its contour under the following
separate conditions: (a) confinement of the chain to a sphere of radius D, and
(b) modulation of its dynamics by colored Gaussian noise. Among other results,
we find that in case (a) when D is much smaller than the size of the chain,
t_{c}\simND^{2}, and that in case (b), t_{c}\simN^{2/(2-2H)}, H being a number
between 1/2 and 1 that characterizes the decay of the noise correlations. H is
not known \`a priori, but values of about 0.7 have been used in the successful
characterization of protein conformational dynamics. At this value of H
(selected for purposes of illustration), t_{c}\simN^3.4, the high scaling
exponent reflecting the slow relaxation of the chain in a viscoelastic medium
On solutions of a class of non-Markovian Fokker-Planck equations
We show that a formal solution of a rather general non-Markovian
Fokker-Planck equation can be represented in a form of an integral
decomposition and thus can be expressed through the solution of the Markovian
equation with the same Fokker-Planck operator. This allows us to classify
memory kernels into safe ones, for which the solution is always a probability
density, and dangerous ones, when this is not guaranteed. The first situation
describes random processes subordinated to a Wiener process, while the second
one typically corresponds to random processes showing a strong ballistic
component. In this case the non-Markovian Fokker-Planck equation is only valid
in a restricted range of parameters, initial and boundary conditions.Comment: A new ref.12 is added and discusse
Competition of Mesoscales and Crossover to Tricriticality in Polymer Solutions
We show that the approach to asymptotic fluctuation-induced critical behavior
in polymer solutions is governed by a competition between a correlation length
diverging at the critical point and an additional mesoscopic length-scale, the
radius of gyration. Accurate light-scattering experiments on polystyrene
solutions in cyclohexane with polymer molecular weights ranging from 200,000 up
to 11.4 million clearly demonstrate a crossover between two universal regimes:
a regime with Ising asymptotic critical behavior, where the correlation length
prevails, and a regime with tricritical theta-point behavior determined by a
mesoscopic polymer-chain length.Comment: 4 pages in RevTeX with 4 figure
Some theoretical studies on concurrent events in photoelectron spectroscopy
Concurrent events in photoelecron spectroscopy such as photoionisation, shake-up and shake-off transitions are studied using atomic wavefunctions recently developed by one of the authors and the concept of the Slater transition state. Various transition energies and intensities are calculated to test the efficiency of the wave-functions and the applicability of the transition state method to these processes. It is concluded that the method is reliable enough to be useful in the assignment of these transitions in the experimental spectrum
The production and detoxification of a potent cytotoxin, nitric oxide, by pathogenic enteric bacteria
The nitrogen cycle is based on several redox reactions that are mainly accomplished by prokaryotic organisms, some archaea and a few eukaryotes, which use these reactions for assimilatory, dissimilatory or respiratory purposes. One group is the Enterobacteriaceae family of Gammaproteobacteria, which have their natural habitats in soil, marine environments or the intestines of humans and other warm-blooded animals. Some of the genera are pathogenic and usually associated with intestinal infections. Our body possesses several physical and chemical defence mechanisms to prevent pathogenic enteric bacteria from invading the gastrointestinal tract. One response of the innate immune system is to activate macrophages, which produce the potent cytotoxin nitric oxide (NO). However, some pathogens have evolved the ability to detoxify NO to less toxic compounds, such as the neuropharmacological agent and greenhouse gas nitrous oxide (N2O), which enables them to overcome the host's attack. The same mechanisms may be used by bacteria producing NO endogenously as a by-product of anaerobic nitrate respiration. In the present review, we provide a brief introduction into the NO detoxification mechanisms of two members of the Enterobacteriaceae family: Escherichia coli and Salmonella enterica serovar Typhimurium. These are discussed as comparative non-pathogenic and pathogenic model systems in order to investigate the importance of detoxifying NO and producing N2O for the pathogenicity of enteric bacteria
Salmonella Pathogenesis and Processing of Secreted Effectors by Caspase-3
The enteric pathogen Salmonella enterica serovar Typhimurium causes food poisoning resulting in gastroenteritis. The S. Typhimurium effector Salmonella invasion protein A (SipA) promotes gastroenteritis by functional motifs that trigger either mechanisms of inflammation or bacterial entry. During infection of intestinal epithelial cells, SipA was found to be responsible for the early activation of caspase-3, an enzyme that is required for SipA cleavage at a specific recognition motif that divided the protein into its two functional domains and activated SipA in a manner necessary for pathogenicity. Other caspase-3 cleavage sites identified in S. Typhimurium appeared to be restricted to secreted effector proteins, which indicates that this may be a general strategy used by this pathogen for processing of its secreted effectors
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