Coarse-grained model of entropic allostery

Many signaling functions in molecular biology require proteins to bind to substrates such as DNA in response to environmental signals such as the simultaneous binding to a small molecule. Examples are repressor proteins which may transmit information via a conformational change in response to the ligand binding. An alternative entropic mechanism of "allostery" suggests that the inducer ligand changes the intramolecular vibrational entropy, not just the mean static structure. We present a quantitative, coarse-grained model of entropic allostery, which suggests design rules for internal cohesive potentials in proteins employing this effect. It also addresses the issue of how the signal information to bind or unbind is transmitted through the protein. The model may be applicable to a wide range of repressors and also to signaling in trans-membrane proteins.     

Entropy and magnetocaloric effect in ferrimagnets RCo<Subscript>2</Subscript>

The equations of state for the magnetic and elastic subsystems of a ferrimagnet are obtained in terms of the exchange–striction model. In the formulas derived for magnetic entropy, it is represented as the sum of the contributions of two magnetic sublattices of the ferrimagnet. One of the main characteristics of the magnetocaloric effect, viz., isothermal variation ΔS _iso of the entropy in a magnetic field, is calculated for compounds RCo₂ (R = Er, Ho, Dy) that experience a first-order magnetic phase transition and TbCo₂ that experiences a second-order magnetic phase transition. It is shown that the calculated values of ΔS _iso for these compounds are in satisfactory quantitative agreement with experimental results. The change in the entropy of a ferrimagnet in a strong magnetic field upon a transition from the ferrimagnetic to ferromagnetic ordering is calculated. The peculiarities in the magnetic field dependences of the magnetic entropy of a two-sublattice ferrimagnet are analyzed.     

A method to calculate Boltzmann entropy

A method is proposed to calculate the Boltzmann non equilibrium entropy as a Taylor series expansion in terms of the successive moments of the velocity distribution function. As a first application, the entropy of the BKW solution of the Boltzmann equation is calculated for both even and odd dimensions. The properties of the entropy of the Tjon Wu modeld=2) are studied and a quantitative condition is derived, showing that the McKean conjecture is incorrect. As a second application of the method, the entropy of one of the solutions of the very hard particle model for the Boltzmann equation is also derived.     

A thermodynamic basis for the electronic properties of molten semiconductors: the role of electronic entropy

Abstract

The thermodynamic origin of a relation between features of the phase diagrams and the electronic properties of molten semiconductors is provided. Leveraging a quantitative connection between electronic properties and entropy, a criterion is derived to establish whether a system will retain its semiconducting properties in the molten phase. It is shown that electronic entropy is critical to the thermodynamics of molten semiconductor systems, driving key features of phase diagrams including, for example, miscibility gaps.     

The principle of the maximum entropy method

Abstract

The theoretical background of the maximum entropy method (MEM) when it is applied to restore the electron or nuclear densities from diffraction data is described. In MEM, the concept of “entropy” is introduced to deal with any incompleteness in an observation in a proper way. An incompleteness causes some ambiguities in the results to some extent. The essence of the method is to find a solution which necessarily agrees with the observation, leaving the measure of ambiguities (entropy) maximum. A few results for simple structures with typical types of chemical bonding are also presented.     

Thermodynamics of self-assembly of sodium octanoate: comparison with a fully fluorinated counterpart

The isotherms of conductivity of sodium octanoate were measured and the critical micelle concentration (cmc) and degree of ionization of the micelles, β, determined in a range of temperatures (273–343 K) above the Krafft point. The thermodynamic parameters, Gibbs free energy ΔG _m ⁰, enthalpy ΔH _m ⁰, and entropy ΔS _m ⁰ of micelle formation, were determined from polynomial adjustments of the temperature dependence of cmc and from a proposed thermodynamic model based on the works of Muller [1993, Langmuir, 9, 96] and Rodríguez et al. [2002, J. Colloid Interface Sci., 250, 438]. The increase in heat capacity upon micellization, ΔC _pm ⁰, was estimated from the parameters of the model and the enthalpy—entropy compensation phenomena discussed. Finally, for information on their structural differences, hence to understand their different behaviours, thermodynamic parameters are discussed, comparing the corresponding fluorocarbon compound. A remarkable shift in minimum temperature in the U-shaped curve of cmc versus temperature was found when hydrogen was substituted by fluorine in the hydrophobic chain of the surfactant. This behaviour is a consequence of the special characteristics of the fluorine substituent in the hydrophobic tail and was reflected in the thermodynamic parameters and in the enthalpy—entropy compensation parameters, presenting different intercepts at the same compensation temperature.     

The determination of percentage dissociation of zircon (ZrSiO4) to plasma‐dissociated zircon (ZrO2.SiO2) by Raman spectroscopy

Raman spectroscopy and multivariate calibration techniques are used to determine the percentage conversion of zircon (ZrSiO₄) to plasma‐dissociated zircon, ZrO₂^.SiO₂ (PDZ). The integrated area of a consistent ZrO₂ (monoclinic) Raman band at 477 cm^–1 assigned to the A_g symmetry type from different conversion percentages of the PDZ spectra is used in a multivariate analysis scheme (partial least squares) to develop a predictive model for the subsequent determination of percentage dissociation of zircon to PDZ. In contrast to wet chemical methods, this approach eliminates the use of corrosive acids, e.g. hydrofluoric acid, thus leading to significant reductions in analysis time and material wastage, and it is a quick method that can be used online in a PDZ production facility. These results show best correlation with determination coefficient (R²) values in the range between 99.45 and 99.99% for zircon percentage dissociation in cross‐validation tests. This illustrates not only the versatility of the Raman technique in industrial applications but also the importance of noninvasive testing in the study of zircon and related materials. Copyright © 2011 John Wiley & Sons, Ltd.     

Quantum Entropy of Spin Fields in the Schwarzschild-Anti-de Sitter Black Hole with a Global Monopole

The quantum entropies of gravitational, electromagnetic, neutrino and scalar fields in the static Schwarzschild-anti-de Sitter black hole with a global monopole are investigated by using the brick-wall model. The quantum entropy contain two parts: One is quadratically divergent term which takes a geometric character; the other is spin-dependent, logarithmically divergent terms. The whole expression of the entropy of a spin field does not take the form of the scalar field. PACS: 04.70. Dy, 97.60.Lf     

Quantum Mutual Entropy for a Multilevel Atom Interacting with a Cavity Field

We derive an explicit formula for the quantum mutual entropy as a measure of the total correlations in a multi-level atom interacting with a cavity field. We describe its theoretical basis and discuss its practical relevance. The effect of the number of levels involved on the quantum mutual entropy is demonstrated via examples of three-, four- and five-level atom. Numerical calculations under current experimental conditions are performed and it is found that the number of levels present changes the general features of the correlations dramatically. PACS numbers: 32.80.−t, 42.50.Ct, 03.65.Ud, 03.65.Yz.     

Acoustic classification of Australian anurans based on hybrid spectral-entropy approach

A new hybrid method for automated frog sound identification, using spectral centroid, Shannon entropy and Rényi entropy is proposed. The advantage of using entropy based information theoretic approach for analyzing complexity of bioacoustics signals in animal vocalization is discussed. Sound samples from nine species of Microhylidae frogs are first segmented into syllables. Fourier spectral centroid, Shannon entropy and Rényi entropy of the syllables are then determined. Finally, nonparametric k-th nearest neighbour (k-NN) classifier is used to recognize the frog species based on these three extracted features. Result shows that the k-NN classifier based on these selected features is capable to identify the species of the frogs with an average accuracy of 98%. It is found that the accuracy reduces significantly only when the noise levels higher than −20 dB.     

Thermodynamics of diffusive DM/DE systems

We discuss the energy density, temperature and entropy of dark matter (DM) and dark energy (DE) as functions of the scale factor a in an expanding universe. In a model of non-interacting dark components we repeat a derivation from thermodynamics of the well-known relations between the energy density, entropy and temperature. In particular, the entropy is constant as a consequence of the energy conservation. We consider a model of a DM/DE interaction where the DM energy density increase is proportional to the particle density. In such a model the dependence of the energy density and the temperature on the scale factor a is substantially modified. We discuss (as a realization of the model) DM which consists of relativistic particles diffusing in an environment of DE. The energy gained by the dark matter comes from a cosmological fluid with a negative pressure. We define the entropy and free energy of such a non-equilibrium system. We show that during the universe evolution the entropy of DM is increasing whereas the entropy of DE is decreasing. The total entropy can increase (in spite of the energy conservation) as the DM and DE temperatures are different. We discuss non-equilibrium thermodynamics on the basis of the notion of the relative entropy.     

A comparative assessment of preclinical chemotherapeutic response of tumors using quantitative non-Gaussian diffusion MRI

BackgroundDiffusion-weighted MRI (DWI) signal attenuation is often not mono-exponential (i.e. non-Gaussian diffusion) with stronger diffusion weighting. Several non-Gaussian diffusion models have been developed and may provide new information or higher sensitivity compared with the conventional apparent diffusion coefficient (ADC) method. However the relative merits of these models to detect tumor therapeutic response is not fully clear.MethodsConventional ADC, and three widely-used non-Gaussian models, (bi-exponential, stretched exponential, and statistical model), were implemented and compared for assessing SW620 human colon cancer xenografts responding to barasertib, an agent known to induce apoptosis via polyploidy. Bayesian Information Criterion (BIC) was used for model selection among all three non-Gaussian models.ResultsAll of tumor volume, histology, conventional ADC, and three non-Gaussian DWI models could show significant differences between control and treatment groups after four days of treatment. However, only the non-Gaussian models detected significant changes after two days of treatment. For any treatment or control group, over 65.7% of tumor voxels indicate the bi-exponential model is strongly or very strongly preferred.ConclusionNon-Gaussian DWI model-derived biomarkers are capable of detecting tumor earlier chemotherapeutic response of tumors compared with conventional ADC and tumor volume. The bi-exponential model provides better fitting compared with statistical and stretched exponential models for the tumor and treatment models used in the current work.     

Detecting and quantifying temporal correlations in stochastic resonance via information theory measures

We show that Information Theory quantifiers are suitable tools for detecting and for quantifying noise-induced temporal correlations in stochastic resonance phenomena. We use the Bandt & Pompe (BP) method [Phys. Rev. Lett. 88, 174102 (2002)] to define a probability distribution, P, that fully characterizes temporal correlations. The BP method is based on a comparison of neighboring values, and here is applied to the temporal sequence of residence-time intervals generated by the paradigmatic model of a Brownian particle in a sinusoidally modulated bistable potential. The probability distribution P generated via the BP method has associated a normalized Shannon entropy, H[P], and a statistical complexity measure, C[P], which is defined as proposed by Rosso et al. [Phys. Rev. Lett. 99, 154102 (2007)]. The statistical complexity quantifies not only randomness but also the presence of correlational structures, the two extreme circumstances of maximum knowledge (“perfect order") and maximum ignorance (“complete randomness") being regarded an “trivial", and in consequence, having complexity C = 0. We show that both, H and C, display resonant features as a function of the noise intensity, i.e., for an optimal level of noise the entropy displays a minimum and the complexity, a maximum. This resonant behavior indicates noise-enhanced temporal correlations in the sequence of residence-time intervals. The methodology proposed here has great potential for the precise detection of subtle signatures of noise-induced temporal correlations in real-world complex signals.     

General constraints on the ionic eos

Abstract

From statistical mechanics one obtains exactly, relative to zeros of energy and entropy at zero temperature, several terms in the high-temperature expansion for the ionic contribution to the equation of state. By standard thermodynamics we relate the temperature independent terms of the high-temperature expansion for the entropy and internal energy to the -1 and 0 moments, respectively, of the specific heat. If we assume that we understand the solid region, this exact high-temperature information then paradoxically constrains the area and general shape of the specific heat curve in the difficult region above melting but below ideal gas. We outline this reasoning and a model that realizes the constraints.     

Covalent magnetism in the RFe <Emphasis Type="Bold">6</Emphasis>Ge <Emphasis Type="Bold">6</Emphasis> series

The electronic structure of the RFe ₆ Ge ₆ compounds ( R = Sc, Lu, Ti, Zr, Hf and Nb) of HfFe ₆ Ge ₆ -type structure has been studied using the muffin-tin Korringa-Kohn-Rostoker method in a non-relativistic approach. The chemical bonding is analyzed based on the l-decomposed site projected densities of states. Spin-dependent changes in the R nd- Fe 3d covalent bond are shown to be responsible for the experimentally observed rise in the Fe moment and hyperfine field upon increasing the R valency. The limited quantitative agreement between theoretical and experimental values is interpreted as being due to a non-negligible orbital moment and to a significant asphericity in the spin density at the iron site. The theoretical results also forecast a strong increase of the Ge(2e) transferred hyperfine field with the R valency. Received 20 December 2002 Published online 4 June 2003 RID="a" ID="a"e-mail: Thomas.Mazet@lcsm.uhp-nancy.fr RID="b" ID="b"Associé au CNRS (UMR 7555)     

Preparation, magnetoresistance and magnetocaloric effect of two-layered perovskite La 2.5- x K 0.5+ x Mn 2 O 7+δ

Polycrystalline two-layered perovskite La_2.5-xK_0.5+xMn₂O _{7 + δ} (0 < x < 0.5) samples have been prepared by a modified sol-gel method and their magnetoresistance and magnetocaloric effects have been studied. A large deviation between the metal-insulator (MI) transition temperature (T _ρ ) and the magnetic transition temperature (T_C) is observed. Large magnetoresistance (MR) effects with Δρ/ρ of ∼40% at 12 kOe are obtained in wide temperature ranges. The maximum of the magnetic entropy change peaks at its Curie temperature (T_C), far above its MI transition temperature (T _ρ ). The large magnetic entropy change (∼1.4 J/kg.K) is obtained in the sample La_2.5-xK_0.5+xMn₂O _{7 + δ} (x = 0.35) upon 10 kOe applied magnetic field. Received 2 May 2002 / Received in final form 1st October 2002 Published online 19 December 2002 RID="a" ID="a"e-mail: wzhong@ufp.nju.edu.cn     

Geometry of Quantum Coherence for Two Qubit X States

The geometry of the structure of entanglement and discord for Bell-diagonal states is depicted by Lang and Caves (Phys. Rev. Lett. 105, 150501, 2010). In this paper, we investigate the geometry with respect to several distance-based quantifiers of coherence for Bell-diagonal states. We find that as both l₁ norm and relative entropy of coherence vary continuously from zero to one, their related geometric surfaces move from the region of separable states to the region of entangled states, a fact illustrating intuitively that quantum states with nonzero coherence can be used for entanglement creation. We find the necessary and sufficient conditions that quantum discord of Bell-diagonal states equals to its relative entropy of coherence, and depict the surfaces related to the equality. We give surfaces of relative entropy of coherence for X states. We show the surfaces of dynamics of relative entropy of coherence for Bell-diagonal states under local nondissipative channels and find that all coherences under local nondissipative channels decrease.

     

Low energy phonon spectrum and its parameterization in pure KTaO<Subscript>3</Subscript> below 80 K

High resolution data on low energy phonon branches (acoustic and soft optic) along the three principal symmetry axes in pure KTaO₃ were obtained by cold neutron inelastic scattering between 10 and 80 K. Additional off-principal axis measurements were performed to characterize the dispersion anisotropy (away from the and axes). The parameters of the phenomenological model proposed by Vaks [28] are refined in order to successfully describe the experimental low temperature (10 < T < 100 K) dispersion curves, over an appreciable reciprocal space volume around the zone center ( rlu). The refined model, which involves only 4 temperature-independent adjustable parameters, is intended to serve as a basis for quantitative computations of multiphonon processes. Received: 29 September 1999 and Received in final form 6 January 2000     

Functional Dynamics of Substrate Recognition in TEM Beta-Lactamase

The beta-lactamase enzyme provides effective resistance to beta-lactam antibiotics due to substrate recognition controlled by point mutations. Recently, extended-spectrum and inhibitor-resistant mutants have become a global health problem. Here, the functional dynamics that control substrate recognition in TEM beta-lactamase are investigated using all-atom molecular dynamics simulations. Comparisons are made between wild-type TEM-1 and TEM-2 and the extended-spectrum mutants TEM-10 and TEM-52, both in apo form and in complex with four different antibiotics (ampicillin, amoxicillin, cefotaxime and ceftazidime). Dynamic allostery is predicted based on a quasi-harmonic normal mode analysis using a perturbation scan. An allosteric mechanism known to inhibit enzymatic function in TEM beta-lactamase is identified, along with other allosteric binding targets. Mechanisms for substrate recognition are elucidated using multivariate comparative analysis of molecular dynamics trajectories to identify changes in dynamics resulting from point mutations and ligand binding, and the conserved dynamics, which are functionally important, are extracted as well. The results suggest that the H10-H11 loop (residues 214-221) is a secondary anchor for larger extended spectrum ligands, while the H9-H10 loop (residues 194-202) is distal from the active site and stabilizes the protein against structural changes. These secondary non-catalytically-active loops offer attractive targets for novel noncompetitive inhibitors of TEM beta-lactamase.     

Quantum spherical model in a random field: coherent state path integral approach

By introducing boson operators, a quantum spherical XY model in the presence of a random field has been studied by the coherent state path integral approach. The phase diagram is obtained, and the effects of the random-field fluctuations on the possibilities of the existence of a ferromagnetic phase are discussed. At the critical point, , the order parameter M describing the ordered ferromagnetic phase disappears as .Since the model is equivalent to a Bose system, we also show that the phase transition at zero temperature between the superfluid and the disordered Mott insulator phases occurs at the chemical potential , where J₀ is the strength of the exchange interaction. As the temperature T goes to zero, the asymptotic behavior of the entropy and the specific heat are and , respectively. Received: 20 May 1997 / Accepted: 20 October 1997