A Comparative Kinetic and Thermodynamic Perspective of the sigma-Competition Model in Escherichia coli

Transcription is the most fundamental step in gene expression in any living organism. Various environmental cues help in the maturation of core RNA polymerase (RNAP; alpha(2)beta beta'omega) with different sigma-factors, leading to the directed recruitment of RNAP to different promoter DNA sequences. Thus it is essential to determine the sigma-factors that affect the preferential partitioning of core RNAP among various a-actors, and the role of sigma-switching in transcriptional gene regulation. Further, the macromolecular assembly of holo RNAP takes place in an extremely crowded environment within a cell, and thus far the kinetics and thermodynamics of this molecular recognition process have not been well addressed. In this study we used a site-directed bioaffinity immobilization method to evaluate the relative binding affinities of three different Escherichia coli sigma-factors to the same core RNAP with variations in temperature and ionic strength while emulating the crowded cellular milieu. Our data indicate that the interaction of core RNAP-sigma is susceptible to changes in external stimuli such as osmolytic and thermal stress, and the degree of susceptibility varies among different sigma-factors. This allows for a reversible sigma-switching from housekeeping factors to alternate sigma-factors when the organism senses a change in its physiological conditions.

On isentropic lines and isentropic exponents

The three indicators of isentropic lines, namely, the isentropic index, the ratio of pressure and density p/rho and the derivative (partial derivative p/partial derivative rho)s are investigated for all of the fluids in the RefProp 9.0 program. The behaviour of these three entities is evaluated along the saturated vapour line as well as in the superheated vapour region. There is a distinct demarcation of fluids whose isentropic indices can be less than 1 and others for which this behaviour is absent. The critical molar volume is found to be the characterizing feature. Several other interesting features of those three thermodynamic properties are also highlighted. It is observed that most practical engineering compression and expansion processes occur along the decreasing direction of the sound speed.

Role of Specific Cations and Water Entropy on the Stability of Branched DNA Motif Structures

DNA three-way junctions (TWJs) are important intermediates in various cellular processes and are the simplest of a family of branched nucleic acids being considered as scaffolds for biomolecular nanotechnology. Branched nucleic acids are stabilized by divalent cations such as Mg2+, presumably due to condensation and neutralization of the negatively charged DNA backbone. However, electrostatic screening effects point to more complex solvation dynamics and a large role of interfacial waters in thermodynamic stability. Here, we report extensive computer simulations in explicit water and salt on a model TWJ and use free energy calculations to quantify the role of ionic character and strength on stability. We find that enthalpic stabilization of the first and second hydration shells by Mg2+ accounts for 1/3 and all of the free energy gain in 50% and pure MgCl2 solutions, respectively. The more distorted DNA molecule is actually destabilized in pure MgCl2 compared to pure NaCl. Notably, the first shell, interfacial waters have very low translational and rotational entropy (i.e., mobility) compared to the bulk, an entropic loss that is overcompensated by increased enthalpy from additional electrostatic interactions with Mg2+. In contrast, the second hydration shell has anomalously high entropy as it is trapped between an immobile and bulklike layer. The nonmonotonic entropic signature and long-range perturbations of the hydration shells to Mg2+ may have implications in the molecular recognition of these motifs. For example, we find that low salt stabilizes the parallel configuration of the three-way junction, whereas at normal salt we find antiparallel configurations deduced from the NMR. We use the 2PT analysis to follow the thermodynamics of this transition and find that the free energy barrier is dominated by entropic effects that result from the decreased surface area of the antiparallel form which has a smaller number of low entropy waters in the first monolayer.

Heat fluctuations and coherences in a quantum heat engine

Quantum coherence can affect the thermodynamics of small quantum systems. Coherences have been shown to affect the power generated by a quantum heat engine (QHE) which is coupled to two thermal photon reservoirs and to an additional cavity mode. We show that the fluctuations of the heat exchanged between the QHE and the reservoirs strongly depend on quantum coherence, especially when the engine operates as a refrigerator, i.e., heat current flows from the cold bath to the hot bath. Intriguingly, we find that the ratio of positive and negative (with respect to the thermodynamic force) fluctuations in the heat current satisfies a universal coherence-independent fluctuation theorem.

The curvature of the liquid-vapor reduced pressure curve and its relation with the critical region

For most fluids, there exist a maximum and a minimum in the curvature of the reduced vapor pressure curve, p(r) = p(r)(T-r) (with p(r) = p/p(c) and T-r = T/T-c, p(c) and T-c being the pressure and temperature at the critical point). By analyzing National Institute of Standards and Technology (NIST) data on the liquid-vapor coexistence curve for 105 fluids, we find that the maximum occurs in the reduced temperature range 0.5 <= T-r <= 0.8 while the minimum occurs in the reduced temperature range 0.980 <= T-r <= 0.995. Vapor pressure equations for which d(2)p(r)/dT(r)(2) diverges at the critical point present a minimum in their curvature. Therefore, the point of minimum curvature can be used as a marker for the critical region. By using the well-known Ambrose-Walton (AW) vapor pressure equation we obtain the reduced temperatures of the maximum and minimum curvature in terms of the Pitzer acentric factor. The AW predictions are checked against those obtained from NIST data. (C) 2013 Elsevier Ltd. All rights reserved.

A thermodynamic framework for fatigue crack growth in concrete

The phenomenon of fatigue is commonly observed in majority of concrete structures and it is important to mathematically model it in order to predict their remaining life. An energy approach is adopted in this research by using the framework of thermodynamics wherein the dissipative phenomenon is described by a dissipation potential. An analytical expression is derived for the dissipation potential using the concepts of dimensional analysis and self-similarity to describe a fatigue crack propagation model for concrete. This is validated using available experimental results. Through a sensitivity analysis, the hierarchy of importance of different parameters is highlighted.

Gibbs energy of formation of Ca7V4O17

Thermodynamic properties of Ca7V4O17 are measured for the first time using a solid-state electrochemical cell incorporating single crystal of CaF2 as the electrolyte over the temperature range from (900 to 1175) K. An equimolar mixture of CaO and CaF2 is used as the reference electrode and a mixture of Ca3V2O8, Ca7V4O17 and CaF2 as the measuring electrode. Both the electrodes are placed under flowing oxygen gas at ambient pressure. The standard Gibbs energy change for the reaction: 2Ca(3)V(2)O(8) + CaO -> Ca7V4O17; which is related to the chemical potential of CaO in the two-phase region (Ca3V2O8 + Ca7V4O17) of the pseudo-binary system CaO + V2O5, is obtained from the electromotive force of the cell as: Delta(r)G(o) +/- 127/(J . mol(-1)) = Delta mu(CaO) = -11453 + 8.273(T/K). The derived standard enthalpy of formation of Ca7V4O17 from elements in their normal standard states is ( 8208.97 +/- 8) kJ . mol (1) and its standard entropy is (560.05 +/- 7.5) J . K (1) . mol (1), both at T = 298.15 K. The results indicate that Ca7V4O17 decomposes into Ca3V2O8 and CaO at T = (1384 +/- 3) K.

Gibbs free energy of formation of rhodium sulfides

Using a solid-state electrochemical technique, thermodynamic properties of three sulfide phases (RhS0.882, Rh3S4, Rh2S3) in the binary system (Rh + S) are measured as a function of temperature over the range from (925 to 1275) K. Single crystal CaF2 is used as the electrolyte. The auxiliary electrode consisting of (CaS + CaF2) is designed in such a way that the sulfur chemical potential converts into an equivalent fluorine potential at each electrode. The sulfur potentials at the measuring electrodes are established by the mixtures of (Rh + RhS0.882), (RhS0.882 + Rh3S4) and (Rh3S4 + Rh2S3) respectively. A gas mixture (H-2 + H2S + Ar) of known composition fixes the sulfur potential at the reference electrode. A novel cell design with physical separation of rhodium sulfides in the measuring electrode from CaS in the auxiliary electrode is used to prevent interaction between the two sulfide phases. They equilibrate only via the gas phase in a hermetically sealed reference enclosure. Standard Gibbs energy changes for the following reactions are calculated from the electromotive force of three cells: 2.2667Rh (s) + S-2 (g) -> 2.2667RhS(0.882) (s), Delta(r)G degrees +/- 2330/(J . mol(-1)) = -288690 + 146.18 (T/K), 4.44RhS(0.882) (s) + S-2 (g) -> 1.48Rh(3)S(4) (s), Delta(r)G degrees +/- 2245/(J . mol(-1)) = -245596 + 164.31 (T/K), 4Rh(3)S(4) (s) + S-2 (g) -> 6Rh(2)S(3) (s), Delta(r)G degrees +/- 2490/(J . mol(-1)) = -230957 + 160: 03 (T/K). Standard entropy and enthalpy of formation of rhodium sulfides from elements in their normal standard states at T = 298.15 K are evaluated. (C) 2013 Elsevier Ltd. All rights reserved.

Higher spin cosmology

We construct cosmological solutions of higher spin gravity in 2 + 1 dimensional de Sitter space. We show that a consistent thermodynamics can be obtained for their horizons by demanding appropriate holonomy conditions. This is equivalent to demanding the integrability of the Euclidean boundary conformal field theory partition function, and it reduces to Gibbons-Hawking thermodynamics in the spin-2 case. By using the prescription of Maldacena, we relate the thermodynamics of these solutions to those of higher spin black holes in AdS(3).

Driving force of water entry into hydrophobic channels of carbon nanotubes: entropy or energy?

Spontaneous entry of water molecules inside single-wall carbon nanotubes (SWCNTs) has been confirmed by both simulations and experiments. Using molecular dynamics simulations, we have studied the thermodynamics of filling of a (6,6) carbon nanotube in a temperature range from 273 to 353K and with different strengths of the nanotube-water interaction. From explicit energy and entropy calculations using the two-phase thermodynamics method, we have presented a thermodynamic understanding of the filling behaviour of a nanotube. We show that both the energy and the entropy of transfer decrease with increasing temperature. On the other hand, scaling down the attractive part of the carbon-oxygen interaction results in increased energy of transfer while the entropy of transfer increases slowly with decreasing the interaction strength. Our results indicate that both energy and entropy favour water entry into (6,6) SWCNTs. Our results are compared with those of several recent studies of water entry into carbon nanotubes.

A thermodynamic framework for the evolution of damage in concrete under fatigue

A closed-form expression for the dual of dissipation potential is derived within the framework of irreversible thermodynamics using the principles of dimensional analysis and self-similarity. Through this potential, a damage evolution law is proposed for concrete under fatigue loading using the concepts of damage mechanics in conjunction with fracture mechanics. The proposed law is used to compute damage in a volume element when a member is subjected to fatigue loading. The evolution of damage from microcracking to macrocracking of the entire member is captured through a series of volume elements failing one after the other. The number of loading cycles to failure of the member is obtained as the summation of number of cycles to failure for each individual volume element. A parametric study is conducted to determine the effect of the size of the volume element on the model's prediction of fatigue life. A global damage index is also defined, and the residual moment carrying capacity of damaged beams is evaluated. Through a deterministic sensitivity analysis, it is found that the load range and maximum aggregate size are the most influencing parameters on the fatigue life of a plain concrete beam.

Simultaneous enhancement in mechanical strength, electrical conductivity, and electromagnetic shielding properties in PVDF-ABS blends containing PMMA wrapped multiwall carbon nanotubes

A unique approach was adopted to drive the multiwall carbon nanotubes (MWNTs) to the interface of immiscible PVDF-ABS blends by wrapping the nanotubes with a mutually miscible homopolymer (PMMA). A tailor made interface with an improved stress transfer was achieved in the blends with PMMA wrapped MWNTs. This manifested in an impressive 108% increment in the tensile strength and 48% increment in the Young's modulus with 3 wt% PMMA wrapped MWNTs in striking contrast to the neat blends. As the PMMA wrapped MWNTs localized at the interface of PVDF-ABS blends, the electrical conductivity could be tuned with respect to only MWNTs, which were selectively localized in the PVDF phase, driven by thermodynamics. The electromagnetic shielding properties were assessed using a vector network analyser in a broad range of frequency, X-band (8-12 GHz) and Ku-band (12-18 GHz). Interestingly, enhanced EM shielding was achieved by this unique approach. The blends with only MWNTs shielded the EM waves mostly by reflection however, the blends with PMMA wrapped MWNTs (3 wt%) shielded mostly by absorption (62%). This study opens new avenues in designing materials, which show simultaneous improvement in mechanical, electrical conductivity and EM shielding properties.

Improving the Rigor and Consistency of the Thermodynamic Theory for Clathrate Hydrates through Incorporation of Movement of Water Molecules of Hydrate Lattice

Current applications of statistical thermodynamic theories for clathrate hydrates do not incorporate the translational and rotational movement of water molecules of the hydrate lattice,in a rigorous manner. Previous studies have shown that the movement of water molecules has a significant effect on the properties of clathrate hydrates. In this Article, a method is presented to incorporate the effect of water movement with as much rigor as possible. This method is then used to calculate the Langmuir constant of the guest species in a clathrate hydrate. Unlike previous studies on modeling of clathrate hydrate thermodynamics, the method presented in this paper does not regress either the intermolecular potentials or the properties of the empty hydrate from clathrate phase equilibria data. Also the properties of empty hydrate used in the theory do not depend on the nature and composition of the guest molecules. The predicted phase equilibria from the resulting theory are shown to be highly accurate and thermodynamically consistent by comparing them with the phase equilibria computed directly from molecular simulations.

Crystal landscape in the orcinol:4,4 `-bipyridine system: synthon modularity, polymorphism and transferability of multipole charge density parameters

Polymorphism in the orcinol: 4,4'-bipyridine cocrystal system is analyzed in terms of a robust convergent modular phenol...pyridine supramolecular synthon. Employing the Synthon Based Fragments Approach (SBFA) to transfer the multipole charge density parameters, it is demonstrated that the crystal landscape can be quantified in terms of intermolecular interaction energies in the five crystal forms so far isolated in this complex system. There are five crystal forms. The first has an open, divergent O-H...N based structure with alternating orcinol and bipyridine molecules. The other four polymorphs have different three-dimensional packing but all of them are similar at an interaction level, and are based on a modular O-H...N mediated supramolecular synthon that consists of two orcinol and two bipyridine molecules in a closed, convergent structure. The SBFA method, which depends on the modularity of synthons, provides good agreement between experiment and theory because it takes into account the supramolecular contribution to charge density. The existence of five crystal forms in this system shows that polymorphism in cocrystals need not be considered to be an unusual phenomenon. Studies of the crystal landscape could lead to an understanding of the kinetic pathways that control the crystallization processes, in other words the valleys in the landscape. These pathways are traditionally not considered in exercises pertaining to computational crystal structure prediction, which rather monitors the thermodynamics of the various stable forms in the system, in other words the peaks in the landscape.

Prediction of Fatigue Life in Plain Concrete Using Entropy Production

An energy approach within the framework of thermodynamics is used to model the fatigue process in plain concrete. Fatigue crack growth is an irreversible process associated with an irreversible entropy gain. A closed-form expression for entropy generated during fatigue in terms of energy dissipated is derived using principles of dimensional analysis and self-similarity. An increase in compliance is considered as a measure of damage accumulated during fatigue. The entropy at final fatigue failure is shown to be independent of loading and geometry and is proposed as a material property. A relationship between energy dissipated and number of cycles of fatigue loading is obtained. (C) 2015 American Society of Civil Engineers.