2,553 research outputs found
Relationship between Thermodynamic Driving Force and One-Way Fluxes in Reversible Chemical Reactions
Chemical reaction systems operating in nonequilibrium open-system states
arise in a great number of contexts, including the study of living organisms,
in which chemical reactions, in general, are far from equilibrium. Here we
introduce a theorem that relates forward and re-verse fluxes and free energy
for any chemical process operating in a steady state. This rela-tionship, which
is a generalization of equilibrium conditions to the case of a chemical process
occurring in a nonequilibrium steady state, provides a novel equivalent
definition for chemical reaction free energy. In addition, it is shown that
previously unrelated theories introduced by Ussing and Hodgkin and Huxley for
transport of ions across membranes, Hill for catalytic cycle fluxes, and Crooks
for entropy production in microscopically reversible systems, are united in a
common framework based on this relationship.Comment: 11 page
Stochastic dynamics of macromolecular-assembly networks
The formation and regulation of macromolecular complexes provides the
backbone of most cellular processes, including gene regulation and signal
transduction. The inherent complexity of assembling macromolecular structures
makes current computational methods strongly limited for understanding how the
physical interactions between cellular components give rise to systemic
properties of cells. Here we present a stochastic approach to study the
dynamics of networks formed by macromolecular complexes in terms of the
molecular interactions of their components. Exploiting key thermodynamic
concepts, this approach makes it possible to both estimate reaction rates and
incorporate the resulting assembly dynamics into the stochastic kinetics of
cellular networks. As prototype systems, we consider the lac operon and phage
lambda induction switches, which rely on the formation of DNA loops by proteins
and on the integration of these protein-DNA complexes into intracellular
networks. This cross-scale approach offers an effective starting point to move
forward from network diagrams, such as those of protein-protein and DNA-protein
interaction networks, to the actual dynamics of cellular processes.Comment: Open Access article available at
http://www.nature.com/msb/journal/v2/n1/full/msb4100061.htm
The overlap parameter across an inverse first order phase transition in a 3D spin-glass
We investigate the thermodynamic phase transition taking place in the
Blume-Capel model in presence of quenched disorder in three dimensions (3D). In
particular, performing Exchange Montecarlo simulations, we study the behavior
of the order parameters accross the first order phase transition and its
related coexistence region. This transition is an Inverse Freezing.Comment: 9 pages, 6 figures, Contribution to the XII International Workshop on
Complex System
Selective-pivot sampling of radial distribution functions in asymmetric liquid mixtures
We present a Monte Carlo algorithm for selectively sampling radial
distribution functions and effective interaction potentials in asymmetric
liquid mixtures. We demonstrate its efficiency for hard-sphere mixtures, and
for model systems with more general interactions, and compare our simulations
with several analytical approximations. For interaction potentials containing a
hard-sphere contribution, the algorithm yields the contact value of the radial
distribution function.Comment: 5 pages, 5 figure
Transplantation Pneumonia
A clinically distinct pneumonitis occurred in six renal transplant recipients receiving azathioprine and prednisone immunosuppressive therapy. The patients ranged in age from 3 to 20 years. The onset was 42 to 102 days postoperatively, coinciding with decrease in prednisone dosage below approximately 1 mg per kilogram of body weight per day. Mild nonproductive cough, fever, and cynanosis were present. Chest x-rays demonstrated extensive hazy to nodular infiltrates usually involving both hila and lower lung fields. Cold agglutinins were present in five patients. Pulmonary function studies demonstrated an alveolar capillary block. The duration of illness was 12 to 34 days and was not influenced by antibiotic therapy. Autopsy of the single case in which death occurred revealed Pneumocystis carinii pneumonia and disseminated cytomegalic inclusion-body disease. © 1964, American Medical Association. All rights reserved
Finite-size scaling considerations on the ground state microcanonical temperature in entropic sampling simulations
In this work we discuss the behavior of the microcanonical temperature
obtained by means of numerical entropic
sampling studies. It is observed that in almost all cases the slope of the
logarithm of the density of states is not infinite in the ground state,
since as expected it should be directly related to the inverse temperature
. Here we show that these finite slopes are in fact due to
finite-size effects and we propose an analytic expression for the
behavior of when . To
test this idea we use three distinct two-dimensional square lattice models
presenting second-order phase transitions. We calculated by exact means the
parameters and for the two-states Ising model and for the and
states Potts model and compared with the results obtained by entropic sampling
simulations. We found an excellent agreement between exact and numerical
values. We argue that this new set of parameters and represents an
interesting novel issue of investigation in entropic sampling studies for
different models
Mean-field cooperativity in chemical kinetics
We consider cooperative reactions and we study the effects of the interaction
strength among the system components on the reaction rate, hence realizing a
connection between microscopic and macroscopic observables. Our approach is
based on statistical mechanics models and it is developed analytically via
mean-field techniques. First of all, we show that, when the coupling strength
is set positive, the model is able to consistently recover all the various
cooperative measures previously introduced, hence obtaining a single unifying
framework. Furthermore, we introduce a criterion to discriminate between weak
and strong cooperativity, based on a measure of "susceptibility". We also
properly extend the model in order to account for multiple attachments
phenomena: this is realized by incorporating within the model -body
interactions, whose non-trivial cooperative capability is investigated too.Comment: 25 pages, 4 figure
Deterministic mechanical model of T-killer cell polarization reproduces the wandering of aim between simultaneously engaged targets
T-killer cells of the immune system eliminate virus-infected and tumorous cells through direct cell-cell interactions. Reorientation of the killing apparatus inside the T cell to the T-cell interface with the target cell ensures specificity of the immune response. The killing apparatus can also oscillate next to the cell-cell interface. When two target cells are engaged by the T cell simultaneously, the killing apparatus can oscillate between the two interface areas. This oscillation is one of the most striking examples of cell movements that give the microscopist an unmechanistic impression of the cell's fidgety indecision. We have constructed a three-dimensional, numerical biomechanical model of the molecular-motor-driven microtubule cytoskeleton that positions the killing apparatus. The model demonstrates that the cortical pulling mechanism is indeed capable of orienting the killing apparatus into the functional position under a range of conditions. The model also predicts experimentally testable limitations of this commonly hypothesized mechanism of T-cell polarization. After the reorientation, the numerical solution exhibits complex, multidirectional, multiperiodic, and sustained oscillations in the absence of any external guidance or stochasticity. These computational results demonstrate that the strikingly animate wandering of aim in T-killer cells has a purely mechanical and deterministic explanation. © 2009 Kim, Maly
Non-Perturbative Renormalization Group for Simple Fluids
We present a new non perturbative renormalization group for classical simple
fluids. The theory is built in the Grand Canonical ensemble and in the
framework of two equivalent scalar field theories as well. The exact mapping
between the three renormalization flows is established rigorously. In the Grand
Canonical ensemble the theory may be seen as an extension of the Hierarchical
Reference Theory (L. Reatto and A. Parola, \textit{Adv. Phys.}, \textbf{44},
211 (1995)) but however does not suffer from its shortcomings at subcritical
temperatures. In the framework of a new canonical field theory of liquid state
developed in that aim our construction identifies with the effective average
action approach developed recently (J. Berges, N. Tetradis, and C. Wetterich,
\textit{Phys. Rep.}, \textbf{363} (2002))
Use of a Semi-field System to Evaluate the Efficacy of Topical Repellents under user Conditions Provides a Disease Exposure free Technique Comparable with Field Data.
Before topical repellents can be employed as interventions against arthropod bites, their efficacy must be established. Currently, laboratory or field tests, using human volunteers, are the main methods used for assessing the efficacy of topical repellents. However, laboratory tests are not representative of real life conditions under which repellents are used and field-testing potentially exposes human volunteers to disease. There is, therefore, a need to develop methods to test efficacy of repellents under real life conditions while minimizing volunteer exposure to disease. A lotion-based, 15% N, N-Diethyl-3-methylbenzamide (DEET) repellent and 15% DEET in ethanol were compared to a placebo lotion in a 200 sq m (10 m x 20 m) semi-field system (SFS) against laboratory-reared Anopheles arabiensis mosquitoes and in full field settings against wild malaria vectors and nuisance-biting mosquitoes. The average percentage protection against biting mosquitoes over four hours in the SFS and field setting was determined. A Poisson regression model was then used to determine relative risk of being bitten when wearing either of these repellents compared to the placebo. Average percentage protection of the lotion-based 15% DEET repellent after four hours of mosquito collection was 82.13% (95% CI 75.94-88.82) in the semi-field experiments and 85.10% (95% CI 78.97-91.70) in the field experiments. Average percentage protection of 15% DEET in ethanol after four hours was 71.29% (CI 61.77-82.28) in the semi-field system and 88.24% (84.45-92.20) in the field. Semi-field evaluation results were comparable to full-field evaluations, indicating that such systems could be satisfactorily used in measuring efficacy of topically applied mosquito repellents, thereby avoiding risks of exposure to mosquito-borne pathogens, associated with field testing
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