Electrostatic Contributions to the Thermodynamics of Ribonuclease P Protein Folding

Electrostatic interactions are of fundamental importance in determining the structure and stability of macromolecules. For example, charge-charge interactions modulate the folding and binding of proteins and influence protein solubility. Electrostatic interactions are highly variable and can be both favorable and unfavorable. The ability to quantify these interactions is challenging but vital to understanding the detailed balance and major roles that they have in different proteins and biological processes. Measuring pKa values of ionizable groups provides a sensitive method for experimentally probing the electrostatic properties of a protein.

pKa values report the free energy of site-specific proton binding and provide a direct means of studying protein folding and pH-dependent stability. Using a combination of NMR, circular dichroism, and fluorescence spectroscopy along with singular value decomposition, we investigated the contributions of electrostatic interactions to the thermodynamic stability and folding of the protein subunit of Bacillus subtilis ribonuclease P, P protein. Taken together, the results suggest that unfavorable electrostatics alone do not account for the fact that P protein is intrinsically unfolded in the absence of ligand because the pKa differences observed between the folded and unfolded state are small. Presumably, multiple factors encoded in the P protein sequence account for its IUP property, which may play an important role in its function.

On thermodynamics in the primary power conversion of oscillating water column wave energy converters

The paper presents an investigation to the thermodynamics of the air flow in the air chamber for the oscillating water column wave energy converters, in which the oscillating water surface in the water column pressurizes or de-pressurises the air in the chamber. To study the thermodynamics and the compressibility of the air in the chamber, a method is developed in this research: the power take-off is replaced with an accepted semi-empirical relationship between the air flow rate and the oscillating water column chamber pressure, and the thermodynamic process is simplified as an isentropic process. This facilitates the use of a direct expression for the work done on the power take-off by the flowing air and the generation of a single differential equation that defines the thermodynamic process occurring inside the air chamber. Solving the differential equation, the chamber pressure can be obtained if the interior water surface motion is known or the chamber volume (thus the interior water surface motion) if the chamber pressure is known. As a result, the effects of the air compressibility can be studied. Examples given in the paper have shown the compressibility, and its effects on the power losses for large oscillating water column devices.

Non-equilibrium thermodynamics of harmonically trapped bosons

We apply the framework of non-equilibrium quantum thermodynamics to the physics of quenched small-size bosonic quantum gases in a harmonic trap. By studying the temporal behaviour of the Loschmidt echo and of the atomic density profile within the trap, which are informative of the non-equilibrium physics and the correlations among the particles, we establish a link with the statistics of (irreversible) work done on the system. This highlights interesting connections between the degree of inter-particle entanglement and the non-equilibrium thermodynamics of the system.

Nonequilibrium critical scaling from quantum thermodynamics

The emerging field of quantum thermodynamics is contributing important results and insights into archetypal many-body problems, including quantum phase transitions. Still, the question whether out-of-equilibrium quantities, such as fluctuations of work, exhibit critical scaling after a sudden quench in a closed system has remained elusive. Here, we take a novel approach to the problem by studying a quench across an impurity quantum critical point. By performing density matrix renormalization group computations on the two-impurity Kondo model, we are able to establish that the irreversible work produced in a quench exhibits finite-size scaling at quantum criticality. This scaling faithfully predicts the equilibrium critical exponents for the crossover length and the order parameter of the model, and, moreover, implies a new exponent for the rescaled irreversible work. By connecting the irreversible work to the two-impurity spin correlation function, our findings can be tested experimentally.

Thermodynamics and Heat Transport of doped Spin-Ice Materials

In this thesis the low-temperature magnetism of the spin-ice systems Dy2Ti2O7 and Ho2Ti2O7 is investigated. In general, a clear experimental evidence for a sizable magnetic contribution kappa_{mag} to the low-temperature, zero-field heat transport of both spin-ice materials is observed. This kappa_{mag} can be attributed to the magnetic monopole excitations, which are highly mobile in zero field and are suppressed by a rather small external field resulting in a drop of kappa(H). Towards higher magnetic fields, significant field dependencies of the phononic heat conductivities kappa_{ph}(H) of Ho2Ti2O7 and Dy2Ti2O7 are found, which are, however, of opposite signs, as it is also found for the highly dilute reference materials (Ho0.5Y0.5)2Ti2O7 and (Dy0.5Y0.5)2Ti2O7. The dominant effect in the Ho-based materials is the scattering of phonons by spin flips which appears to be significantly stronger than in the Dy-based materials. Here, the thermal conductivity is suppressed due to enhanced lattice distortions observed in the magnetostriction. Furthermore, the thermal conductivity of Dy2Ti2O7 has been investigated concerning strong hysteresis effects and slow-relaxation processes towards equilibrium states in the low-temperature and low-field regime. The thermal conductivity in the hysteretic regions slowly relaxes towards larger values suggesting that there is an additional suppression of the heat transport by disorder in the non-equilibrium states. The equilibration can even be governed by the heat current for particular configurations. A special focus was put on the dilution series Dy2Ti2O7x. From specific heat measurements, it was found that the ultra-slow thermal equilibration in pure spin ice Dy2Ti2O7 is rapidly suppressed upon dilution with non-magnetic yttrium and vanishes completely for x>=0.2 down to the lowest accessible temperatures. In general, the low-temperature entropy of (Dy1-xYx)2Ti2O7, considerably decreases with increasing x, whereas its temperature-dependence drastically increases. Thus, it could be clarified that there is no experimental evidence for a finite zero-temperature entropy in (Dy1-xYx)2Ti2O7 above x>=0.2, in clear contrast to the finite residual entropy S_{P}(x) expected from a generalized Pauling approximation. A similar discrepancy is also present between S_{P}(x) and the low-temperature entropy obtained by Monte Carlo simulations, which reproduce the experimental data from 25 K down to 0.7 K, whereas the data at 0.4 K are overestimated. A straightforward description of the field-dependence kappa(H) of the dilution series with qualitative models justifies the extraction of kappa_{mag}. It was observed that kappa_{mag} systematically scales with the degree of dilution and its low-field decrease is related to the monopole excitation energy. The diffusion coefficient D_{mag} for the monopole excitations was calculated by means of c_{mag} and kappa_{mag}. It exhibits a broad maximum around 1.6 K and is suppressed for T<=0.5 K, indicating a non-degenerate ground state in the long-time limit, and in the high-temperature range for T>=4 K where spin-ice physics is eliminated. A mean-free path of 0.3 mum is obtained for Dy2Ti2O7 at about 1 K within the kinetic gas theory.

Desorption isotherms and thermodynamics properties of anchovy in natura and enzymatic modified paste

The thermodynamic properties of anchovy fillets and enzymatic modified pastes in two hydrolysis degrees (3% HD and 14% HD), at 50, 60 and 70 C were evaluated. The GAB model was used to calculate the values of the monolayer moisture content and the thermodynamic properties of the samples. The enzymatic modification led to the increases of the superficial area and differential enthalpies, and decrease of the differential entropies in relation the samples in natura. The enthalpy–entropy compensation showed that the process was controlled by the enthalpy, it was only spontaneous for the samples in natura. Pore size decreased with enzymatic modification, and all samples were in the limit of region between micropores and mesopores (<2 nm) for moisture content of 15%, and mesopores (from 2 to 50 nm) to moisture content above 15%.

Topics in equilibrium and nonequilibrium thermodynamics: computing crystalline free energies and engineering Maxwell’s demon.

This dissertation covers two separate topics in statistical physics. The first part of the dissertation focuses on computational methods of obtaining the free energies (or partition functions) of crystalline solids. We describe a method to compute the Helmholtz free energy of a crystalline solid by direct evaluation of the partition function. In the many-dimensional conformation space of all possible arrangements of N particles inside a periodic box, the energy landscape consists of localized islands corresponding to different solid phases. Calculating the partition function for a specific phase involves integrating over the corresponding island. Introducing a natural order parameter that quantifies the net displacement of particles from lattices sites, we write the partition function in terms of a one-dimensional integral along the order parameter, and evaluate this integral using umbrella sampling. We validate the method by computing free energies of both face-centered cubic (FCC) and hexagonal close-packed (HCP) hard sphere crystals with a precision of $10^{-5}k_BT$ per particle. In developing the numerical method, we find several scaling properties of crystalline solids in the thermodynamic limit. Using these scaling properties, we derive an explicit asymptotic formula for the free energy per particle in the thermodynamic limit. In addition, we describe several changes of coordinates that can be used to separate internal degrees of freedom from external, translational degrees of freedom. The second part of the dissertation focuses on engineering idealized physical devices that work as Maxwell's demon. We describe two autonomous mechanical devices that extract energy from a single heat bath and convert it into work, while writing information onto memory registers. Additionally, both devices can operate as Landauer's eraser, namely they can erase information from a memory register, while energy is dissipated into the heat bath. The phase diagrams and the efficiencies of the two models are solved and analyzed. These two models provide concrete physical illustrations of the thermodynamic consequences of information processing.

Two-State Thermodynamics of Supercooled Water

Water has been called the “most studied and least understood” of all liquids, and upon supercooling its behavior becomes even more anomalous. One particularly fruitful hypothesis posits a liquid-liquid critical point terminating a line of liquid-liquid phase transitions that lies just beyond the reach of experiment. Underlying this hypothesis is the conjecture that there is a competition between two distinct hydrogen-bonding structures of liquid water, one associated with high density and entropy and the other with low density and entropy. The competition between these structures is hypothesized to lead at very low temperatures to a phase transition between a phase rich in the high-density structure and one rich in the low-density structure. Equations of state based on this conjecture have given an excellent account of the thermodynamic properties of supercooled water. In this thesis, I extend that line of research. I treat supercooled aqueous solutions and anomalous behavior of the thermal conductivity of supercooled water. I also address supercooled water at negative pressures, leading to a framework for a coherent understanding of the thermodynamics of water at low temperatures. I supplement analysis of experimental results with data from the TIP4P/2005 model of water, and include an extensive analysis of the thermodynamics of this model.

THERMODYNAMICS AND APPLICATION OF A PAIR OF SYNTHETIC NUCLEOBASES FROM ARTIFICIALLY EXPANDED GENETIC INFORMATION SYSTEM

UV-melting experiments were performed on 9-mer duplexes containing a pair of synthetic nucleobases P·Z, two members of Expanded Genetic Information System (AEGIS), or P, Z containing mismatches. Enthalpy, entropy and free energy change were derived from simulation using two-state transition model. Nearest neighbor thermodynamic parameters of trimers or tetramers containing P·Z pair or P, Z containing mismatches were derived based on known nearest neighbor parameters. Proposed structures based on thermodynamic parameters are discussed. An application using P·Z pair as reverse selection tool of desired nucleic acid secondary structure is described.

Liquid Mixtures Involving Hydrogenated and Fluorinated Alcohols: Thermodynamics, Spectroscopy, and Simulation

This article reports a combined thermodynamic, spectroscopic, and computational study on the interactions and structure of binary mixtures of hydrogenated and fluorinated substances that simultaneously interact through strong hydrogen bonding. Four binary mixtures of hydrogenated and fluorinated alcohols have been studied, namely, (ethanol + 2,2,2-trifluoroethanol (TFE)), (ethanol + 2,2,3,3,4,4,4-heptafluoro-1-butanol), (1-butanol (BuOH) + TFE), and (BuOH + 2,2,3,3,4,4,4-heptafluoro-1-butanol). Excess molar volumes and vibrational spectra of all four binary mixtures have been measured as a function of composition at 298 K, and molecular dynamics simulations have been performed. The systems display a complex behavior when compared with mixtures of hydrogenated alcohols and mixtures of alkanes and perfluoroalkanes. The combined analysis of the results from different approaches indicates that this results from a balance between preferential hydrogen bonding between the hydrogenated and fluorinated alcohols and the unfavorable dispersion forces between the hydrogenated and fluorinated chains. As the chain length increases, the contribution of dispersion increases and overcomes the contribution of H-bonds. In terms of the liquid structure, the simulations suggest the possibility of segregation between the hydrogenated and fluorinated segments, a hypothesis corroborated by the spectroscopic results. Furthermore, a quantitative analysis of the infrared spectra reveals that the presence of fluorinated groups induces conformational changes in the hydrogenated chains from the usually preferred all-trans to more globular arrangements involving gauche conformations. Conformational rearrangements at the CCOH dihedral angle upon mixing are also disclosed by the spectra.

A deep learning model via thermodynamics and condensed matter physics

Deep Learning architectures give brilliant results in a large variety of fields, but a comprehensive theoretical description of their inner functioning is still lacking. In this work, we try to understand the behavior of neural networks by modelling in the frameworks of Thermodynamics and Condensed Matter Physics. We approach neural networks as in a real laboratory and we measure the frequency spectrum and the entropy of the weights of the trained model. The stochasticity of the training occupies a central role in the dynamics of the weights and makes it difficult to assimilate neural networks to simple physical systems. However, the analogy with Thermodynamics and the introduction of a well defined temperature leads us to an interesting result: if we eliminate from a CNN the "hottest" filters, the performance of the model remains the same, whereas, if we eliminate the "coldest" ones, the performance gets drastically worst. This result could be exploited in the realization of a training loop which eliminates the filters that do not contribute to loss reduction. In this way, the computational cost of the training will be lightened and more importantly this would be done by following a physical model. In any case, beside important practical applications, our analysis proves that a new and improved modeling of Deep Learning systems can pave the way to new and more efficient algorithms.

Thermodynamics of hydrogen absorption in Mg thin films and multilayers studied by electrochemical method

Electrochemical hydrogen loading is a technique used to produce and study the hydrogenation in metals starting from a liquid solution containing water. It is a possible alternative to another, well-established technique which loads hydrogen starting from its gas phase. In this work, the electrochemical method is used to understand the fundamental thermodynamics of hydrogen loading in constraint systems such as thin films on substrates, and possibly distinguish the role of interfaces, stresses and microstructure during the hydrogenation process. The systems under study are thin films of Pd, Mg/Pd, and Ti/Mg multilayers. Possible future technological applications may be in the field of hydrogen storage and hydrogen sensors. Towards the end, the experimental setup is modified by introducing an automatic relay. This change leads to improvements in the data analysis and in the attainable information on the kinetics of the systems.

Diagramas de Ellingham e de Van't Hoff: algumas considerações

The main subject of this article is to show the parallelism betwen the Ellingham and Van't Hoff diagrams. The first one is a graphic representation of the changes in the standard Gibbs free energy (deltarGtheta) as a function of T and was introduced by Ellingham in 1944, in order to study metallurgic processes involving oxides and sulphides. On the other hand, the Van't Hoff diagram is a representation of the function ln K versus (1/T). The equivalence between both diagrams is easily demonstrated, making simple mathematical manipulations. In order to show the parallelism between both diagrams, they are presented briefly and two examples are discussed. The comparison of the both diagrams surely will be helpful to students and teachers in their learning and teaching activities, and will certainly enrich important aspects of chemical thermodynamics.

A quantidade de matéria nas ciências clássicas

The chemical amount values vary in a discrete or continuous form, depending on the approach used to describe the system. In classical sciences, the chemical amount is a property of the macroscopic system and, like any other property of the system, it varies continuously. This is neither inconsistent with the concept of indivisible particles forming the system, nor a mere approximation, but it is a sound concept which enables the use of differential calculus, for instance, in chemical thermodynamics. It is shown that the fundamental laws of chemistry are absolutely compatible to the continuous concept of the chemical amount.