327 research outputs found
Metabolic enzymes from psychrophilic bacteria: Challenge of adaptation to low temperatures in ornithine carbamoyltransferase from Moritella abyssi
The enzyme ornithine carbamoyltransferase (OTCase) of Motitella abyssi (OTCase(Mab)), a new, strictly psychrophilic and piezophilic bacterial species, was purified. OTCase(Mab) displays maximal activity at rather low temperatures (23 to 25degreesC) compared to other cold-active enzymes and is much less thermoresistant than its homologues from Escherichia coli or thermophilic procaryotes. In vitro the enzyme is in equilibrium between a trimeric state and a dodecameric, more stable state. The melting point and denaturation enthalpy changes for the two forms are considerably lower than the corresponding values for the dodecameric Pyrococcus furiosus OTCase and for a thermolabile trimeric mutant thereof. OTCase(Mab) displays higher K-m values for ornithine and carbamoyl phosphate than mesophilic and thermophilic OTCases and is only weakly inhibited by the bisubstrate analogue delta-N-phosphonoacetyl-L-ornithine (PALO). OTCase(Mab) differs from other, nonpsychrophilic OTCases by substitutions in the most conserved motifs, which probably contribute to the comparatively high K-m values and the lower sensitivity to PALO. The K. for ornithine, however, is substantially lower at low temperatures. A survey of the catalytic efficiencies (k(cat)/K-m) of OTCases adapted to different temperatures showed that OTCase(Mab) activity remains suboptimal at low temperature despite the 4.5-fold decrease in the K-m value for ornithine observed when the temperature is brought from 20 to 5degreesC. OTCase(Mab) adaptation to cold indicates a trade-off between affinity and catalytic velocity, suggesting that optimization of key metabolic enzymes at low temperatures may be constrained by natural limits
Negative diffraction pattern dynamics in nonlinear cavities with left-handed materials
We study a ring cavity filled with a slab of a right-handed material and a
slab of a left-handed material. Both layers are assumed to be nonlinear Kerr
media. First, we derive a model for the propagation of light in a left-handed
material. By constructing a mean-field model, we show that the sign of
diffraction can be made either positive or negative in this resonator,
depending on the thicknesses of the layers. Subsequently, we demonstrate that
the dynamical behavior of the modulation instability is strongly affected by
the sign of the diffraction coefficient. Finally, we study the dissipative
structures in this resonator and reveal the predominance of a two-dimensional
up-switching process over the formation of spatially periodic structures,
leading to the truncation of the homogeneous hysteresis cycle.Comment: 8 pages, 5 figure
Energy and entropy of relativistic diffusing particles
We discuss energy-momentum tensor and the second law of thermodynamics for a
system of relativistic diffusing particles. We calculate the energy and entropy
flow in this system. We obtain an exact time dependence of energy, entropy and
free energy of a beam of photons in a reservoir of a fixed temperature.Comment: 14 pages,some formulas correcte
Emergent Hydrodynamics in Integrable Quantum Systems Out of Equilibrium
Understanding the general principles underlying strongly interacting quantum states out of equilibrium is one of the most important tasks of current theoretical physics. With experiments accessing the intricate dynamics of many-body quantum systems, it is paramount to develop powerful methods that encode the emergent physics. Up to now, the strong dichotomy observed between integrable and nonintegrable evolutions made an overarching theory difficult to build, especially for transport phenomena where space-time profiles are drastically different. We present a novel framework for studying transport in integrable systems: hydrodynamics with infinitely many conservation laws. This bridges the conceptual gap between integrable and nonintegrable quantum dynamics, and gives powerful tools for accurate studies of space-time profiles. We apply it to the description of energy transport between heat baths, and provide a full description of the current-carrying nonequilibrium steady state and the transition regions in a family of models including the Lieb-Liniger model of interacting Bose gases, realized in experiments
Generic stability of dissipative non-relativistic and relativistic fluids
The linear stability of the homogeneous equilibrium of non-relativistic
fluids with mass flux and special relativistic fluids with the absolute value
of the energy vector as internal energy is investigated. It is proved that the
equilibrium is asymptotically stable in both cases due to purely thermodynamic
restrictions; the only requirements are the thermodynamic stability and the
nonnegativity of the transport coefficients.Comment: 22 page
Sand as Maxwell's demon
We consider a dilute gas of granular material inside a box, kept in a
stationary state by shaking. A wall separates the box into two identical
compartments, save for a small hole at some finite height . As the gas is
cooled, a second order phase transition occurs, in which the particles
preferentially occupy one side of the box. We develop a quantitative theory of
this clustering phenomenon and find good agreement with numerical simulations
Mapping between dissipative and Hamiltonian systems
Theoretical studies of nonequilibrium systems are complicated by the lack of
a general framework. In this work we first show that a transformation
introduced by Ao recently (J. Phys. A {\bf 37}, L25 (2004)) is related to
previous works of Graham (Z. Physik B {\bf 26}, 397 (1977)) and Eyink {\it et
al.} (J. Stat. Phys. {\bf 83}, 385 (1996)), which can also be viewed as the
generalized application of the Helmholtz theorem in vector calculus. We then
show that systems described by ordinary stochastic differential equations with
white noise can be mapped to thermostated Hamiltonian systems. A steady-state
of a dissipative system corresponds to the equilibrium state of the
corresponding Hamiltonian system. These results provides a solid theoretical
ground for corresponding studies on nonequilibrium dynamics, especially on
nonequilibrium steady state. The mapping permits the application of established
techniques and results for Hamiltonian systems to dissipative non-Hamiltonian
systems, those for thermodynamic equilibrium states to nonequilibrium steady
states. We discuss several implications of the present work.Comment: 18 pages, no figure. final version for publication on J. Phys. A:
Math & Theo
Diffuse-interface model for rapid phase transformations in nonequilibrium systems
A thermodynamic approach to rapid phase transformations within a diffuse
interface in a binary system is developed. Assuming an extended set of
independent thermodynamic variables formed by the union of the classic set of
slow variables and the space of fast variables, we introduce finiteness of the
heat and solute diffusive propagation at the finite speed of the interface
advancing. To describe the transformation within the diffuse interface, we use
the phase-field model which allows us to follow the steep but smooth change of
phases within the width of diffuse interface. The governing equations of the
phase-field model are derived for the hyperbolic model, model with memory, and
for a model of nonlinear evolution of transformation within the
diffuse-interface. The consistency of the model is proved by the condition of
positive entropy production and by the outcomes of the fluctuation-dissipation
theorem. A comparison with the existing sharp-interface and diffuse-interface
versions of the model is given.Comment: 15 pages, regular article submitted to Physical Review
Spatial interactions in agent-based modeling
Agent Based Modeling (ABM) has become a widespread approach to model complex
interactions. In this chapter after briefly summarizing some features of ABM
the different approaches in modeling spatial interactions are discussed.
It is stressed that agents can interact either indirectly through a shared
environment and/or directly with each other. In such an approach, higher-order
variables such as commodity prices, population dynamics or even institutions,
are not exogenously specified but instead are seen as the results of
interactions. It is highlighted in the chapter that the understanding of
patterns emerging from such spatial interaction between agents is a key problem
as much as their description through analytical or simulation means.
The chapter reviews different approaches for modeling agents' behavior,
taking into account either explicit spatial (lattice based) structures or
networks. Some emphasis is placed on recent ABM as applied to the description
of the dynamics of the geographical distribution of economic activities, - out
of equilibrium. The Eurace@Unibi Model, an agent-based macroeconomic model with
spatial structure, is used to illustrate the potential of such an approach for
spatial policy analysis.Comment: 26 pages, 5 figures, 105 references; a chapter prepared for the book
"Complexity and Geographical Economics - Topics and Tools", P. Commendatore,
S.S. Kayam and I. Kubin, Eds. (Springer, in press, 2014
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