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 $h$. 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

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

Non-Equilibrium Evolution Thermodynamics Theory

Alternative approach for description of the non-equilibrium phenomena arising in solids at a severe external loading is analyzed. The approach is based on the new form of kinetic equations in terms of the internal and modified free energy. It is illustrated by a model example of a solid with vacancies, for which there is a complete statistical ground. The approach is applied to the description of important practical problem - the formation of fine-grained structure of metals during their treatment by methods of severe plastic deformation. In the framework of two-level two-mode effective internal energy potential model the strengthening curves unified for the whole of deformation range and containing the Hall-Petch and linear strengthening sections are calculated.Comment: 7 pages, 1 figur

Phase-bistable patterns and cavity solitons induced by spatially periodic injection into vertical-cavity surface-emitting lasers

Spatial rocking is a kind of resonant forcing able to convert a elf-oscillatory system into a phase-bistable, pattern forming system, whereby the phase of the spatially averaged oscillation field locks to one of two values differing by π. We propose the spatial rocking in an experimentally relevant system the vertical-cavity surface-emitting laser (VCSEL) and demonstrate its feasibility through analytical and numerical tools applied to a VCSEL model. We show phase bistability, spatial patterns, such as roll patterns, domain walls, and phase (dark-ring) solitons, which could be useful for optical information storage and processing purposes