12,211 research outputs found
Epigenetic regulation of Mash1 expression
Mash1 is a proneural gene important for specifying the neural fate. The Mash1 locus undergoes specific epigenetic changes in ES cells following neural induction. These include the loss of repressive H3K27 trimethylation and acquisition of H3K9 acetylation at the promoter, switch to an early replication timing and repositioning of the locus away from the nuclear periphery. Here I examine the relationship between nuclear localization and gene expression during neural differentiation and the role of the neuronal repressor REST in silencing Mash1 expression in ES cells. Following neural induction of ES cells, I observed that relocation of the Mash1 locus occurs from day 4-6 whereas overt expression begins at day 6. Mash1 expression was unaffected by REST removal in ES cells as well as the locus localization at the nuclear periphery. In contrast bona fide REST target genes were upregulated in REST -/- cells. Interestingly, among REST targets, loci that were more derepressed upon REST removal showed an interior location (Sthatmin, Synaptophysin), while those more resistant to REST withdrawal, showed a peripheral location (BDNF, Calbidin, Complexin). To ask whether the insulator protein CTCF together with the cohesin complex might be involved in regulating Mash1 in ES cells, I performed ChIP analysis of CTCF and cohesin binding across the Mash1 locus in ES cells and used RNAi to deplete CTCF and cohesin expression. A slight increase in the transcription of Mash1 was seen in cells upon Rad21 knock down, although it was not possible to exclude this was a consequence of delayed cell cycle progression. Finally ES cell lines that carried a Mash1 transgene were created as a tool to look at whether activation of Mash1 can affect the epigenetic properties of neighbouring genes
Nonlinear Quantum Evolution Equations to Model Irreversible Adiabatic Relaxation with Maximal Entropy Production and Other Nonunitary Processes
We first discuss the geometrical construction and the main mathematical
features of the maximum-entropy-production/steepest-entropy-ascent nonlinear
evolution equation proposed long ago by this author in the framework of a fully
quantum theory of irreversibility and thermodynamics for a single isolated or
adiabatic particle, qubit, or qudit, and recently rediscovered by other
authors. The nonlinear equation generates a dynamical group, not just a
semigroup, providing a deterministic description of irreversible conservative
relaxation towards equilibrium from any non-equilibrium density operator. It
satisfies a very restrictive stability requirement equivalent to the
Hatsopoulos-Keenan statement of the second law of thermodynamics. We then
examine the form of the evolution equation we proposed to describe multipartite
isolated or adiabatic systems. This hinges on novel nonlinear projections
defining local operators that we interpret as ``local perceptions'' of the
overall system's energy and entropy. Each component particle contributes an
independent local tendency along the direction of steepest increase of the
locally perceived entropy at constant locally perceived energy. It conserves
both the locally-perceived energies and the overall energy, and meets strong
separability and non-signaling conditions, even though the local evolutions are
not independent of existing correlations. We finally show how the geometrical
construction can readily lead to other thermodynamically relevant models, such
as of the nonunitary isoentropic evolution needed for full extraction of a
system's adiabatic availability.Comment: To appear in Reports on Mathematical Physics. Presented at the The
Jubilee 40th Symposium on Mathematical Physics, "Geometry & Quanta", Torun,
Poland, June 25-28, 200
Addendum to "Nonlinear quantum evolution with maximal entropy production"
The author calls attention to previous work with related results, which has
escaped scrutiny before the publication of the article "Nonlinear quantum
evolution with maximal entropy production", Phys.Rev.A63, 022105 (2001).Comment: RevTex-latex2e, 2pgs., no figs.; brief report to appear in the May
2001 issue of Phys.Rev.
Maximal-entropy-production-rate nonlinear quantum dynamics compatible with second law, reciprocity, fluctuation-dissipation, and time-energy uncertainty relations
In view of the recent quest for well-behaved nonlinear extensions of the
traditional Schroedinger-von Neumann unitary dynamics that could provide
fundamental explanations of recent experimental evidence of loss of quantum
coherence at the microscopic level, in this paper, together with a review of
the general features of the nonlinear quantum (thermo)dynamics I proposed in a
series of papers [see references in G.P. Beretta, Found.Phys. 17, 365 (1987)],
I show its exact equivalence with the maximal-entropy-production
variational-principle formulation recently derived in S.
Gheorghiu-Svirschevski, Phys.Rev. A 63, 022105 (2001). In addition, based on
the formalism of general interest I developed for the analysis of composite
systems, I show how the variational derivation can be extended to the case of a
composite system to obtain the general form of my equation of motion, that
turns out to be consistent with the demanding requirements of strong
separability. Moreover, I propose a new intriguing fundamental ansatz: that the
time evolution along the direction of steepest entropy ascent unfolds at the
fastest rate compatible with the time-energy Heisenberg uncertainty relation.
This ansatz provides a possible well-behaved general closure of the nonlinear
dynamics, compatible with the nontrivial requirements of strong separability,
and with no need of new physical constants. In any case, the time-energy
uncertainty relation provides lower bounds to the internal-relaxation-time
functionals and, therefore, upper bounds to the rate of entropy production.Comment: RevTeX; 19 pages; submitted to Phys.Rev.A on Feb.9, 2001; revised
version submitted on Sept.14, 2001 with slightly modified derivation in
Section III, improved discussion on strong separability in Sections X and IX,
added Eqs. 64b, 64c and 11
Steepest Entropy Ascent Model for Far-Non-Equilibrium Thermodynamics. Unified Implementation of the Maximum Entropy Production Principle
By suitable reformulations, we cast the mathematical frameworks of several
well-known different approaches to the description of non-equilibrium dynamics
into a unified formulation, which extends to such frameworks the concept of
Steepest Entropy Ascent (SEA) dynamics introduced by the present author in
previous works on quantum thermodynamics. The present formulation constitutes a
generalization also for the quantum thermodynamics framework. In the SEA
modeling principle a key role is played by the geometrical metric with respect
to which to measure the length of a trajectory in state space. In the near
equilibrium limit, the metric tensor is related to the Onsager's generalized
resistivity tensor. Therefore, through the identification of a suitable metric
field which generalizes the Onsager generalized resistance to the arbitrarily
far non-equilibrium domain, most of the existing theories of non-equilibrium
thermodynamics can be cast in such a way that the state exhibits a spontaneous
tendency to evolve in state space along the path of SEA compatible with the
conservation constraints and the boundary conditions. The resulting unified
family of SEA dynamical models is intrinsically and strongly consistent with
the second law of thermodynamics. Non-negativity of the entropy production is a
readily proved general feature of SEA dynamics. In several of the different
approaches to non-equilibrium description we consider here, the SEA concept has
not been investigated before. We believe it defines the precise meaning and the
domain of general validity of the so-called Maximum Entropy Production
Principle. It is hoped that the present unifying approach may prove useful in
providing a fresh basis for effective, thermodynamically consistent, numerical
models and theoretical treatments of irreversible conservative relaxation
towards equilibrium from far non-equilibrium states.Comment: 15 pages, 4 figures, to appear in Physical Review
Quantum thermodynamic Carnot and Otto-like cycles for a two-level system
From the thermodynamic equilibrium properties of a two-level system with
variable energy-level gap , and a careful distinction between the Gibbs
relation and the energy balance equation , we infer some important aspects of the
second law of thermodynamics and, contrary to a recent suggestion based on the
analysis of an Otto-like thermodynamic cycle between two values of of
a spin-1/2 system, we show that a quantum thermodynamic Carnot cycle, with the
celebrated optimal efficiency , is possible in
principle with no need of an infinite number of infinitesimal processes,
provided we cycle smoothly over at least three (in general four) values of
, and we change not only along the isoentropics, but also
along the isotherms, e.g., by use of the recently suggested maser-laser tandem
technique. We derive general bounds to the net-work to high-temperature-heat
ratio for a Carnot cycle and for the 'inscribed' Otto-like cycle, and represent
these cycles on useful thermodynamic diagrams.Comment: RevTex4, 4 pages, 1 figur
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