FTIR analysis of natural and synthetic collagen

Collagen is the most abundant protein in humans and animals, comprising of one third of the total proteins that accounts for three quarters of the dry weight skin in humans. Collagen containing a range of proteins has been reported for tissue engineering applications, but, only a small number of studies related to chemical structure evaluation of collagen are found in the literature. Collagen can be obtained from both the natural and synthetic sources and offers a wide range of biomedical applications due to its excellent biocompatibility and low immunogenicity. Hence, it is important to identify chemical structural properties of collagen and Fourier transform infrared (FTIR) appears to be a technique of choice to study their chemical structure. This review aims to highlight the use of FTIR to study collagen-based biomaterials, using it for characterization of collagen extracted from various sources. Characterization of collagen-based materials used in wound healing, skin substitutes, derma fillers, and aging of skin, collagen containing drug delivery agents, collagen-based materials used in tissue engineering, bone regeneration, and osteogenic differentiation is discussed in detail. FTIR analysis of collagen-containing materials used for dental applications, cleft-palate, and in alveolar-ridge preservation has also been highlighted.     

Molecular basis of structural make-up of feeds in relation to nutrient absorption in ruminants,revealed with advanced molecular spectroscopy: A review on techniques and models

Progress in ruminant feed research is no more feasible only based on wet chemical analysis, which is merely able to provide information on chemical composition of feeds regardless of their digestive features and nutritive value in ruminants. Studying internal structural make-up of functional groups/feed nutrients is often vital for understanding the digestive behaviors and nutritive values of feeds in ruminant because the intrinsic structure of feed nutrients is more related to its overall absorption. In this article, the detail information on the recent developments in molecular spectroscopic techniques to reveal microstructural information of feed nutrients and the use of nutrition models in regards to ruminant feed research was reviewed. The emphasis of this review was on (1) the technological progress in the use of molecular spectroscopic techniques in ruminant feed research; (2) revealing spectral analysis of functional groups of biomolecules/feed nutrients; (3) the use of advanced nutrition models for better prediction of nutrient availability in ruminant systems; and (4) the application of these molecular techniques and combination of nutrient models in cereals, co-products and pulse crop research. The information described in this article will promote better insight in the progress of research on molecular structural make-up of feed nutrients in ruminants.     

熵驱动下柱状高分子刷螺旋结构的研究

自然界中广泛存在螺旋结构,在特定情形下熵能驱动高分子链形成螺旋结构.本文采用分子动力学方法研究柱状高分子刷吸附在无限长圆柱表面时的构象行为.发现其构象与嫁接支链条数、柱状高分子刷与圆柱表面之间的吸附能密切相关.在较弱的吸附能下,具有较多支链条数的柱状高分子刷能形成完整的螺旋结构,其本质就是熵驱动下形成的螺旋结构.该研究有助于加深对生物大分子螺旋结构的理解.     

Control of Correlation Using Confinement in Case of Quantum System

This article investigates the behavior of a Moshinsky atom in a 1D harmonic trap. Focus is given on the theoretical foundations of confinement and its impact on the correlation between particles in the Moshinsky atom. The investigation begins by illustrating the (de)localization of the probability density function using Shannon entropy. The basics of correlation and interpretation of correlation using tools such as mutual information and statistical correlation coefficients and how these can be quantified are discussed. Then the concept of confinement is explored. The impact of interaction strength and confinement on Shannon entropy, statistical correlation coefficients, and mutual information is investigated. How interaction strength and confinement can be used to induce correlations between previously uncorrelated particles, as well as how they can be used to suppress correlations between previously correlated particles is discussed. Their implications for quantum information processing and quantum simulation are discussed. In conclusion, confinement is a powerful tool for controlling correlations in quantum systems, and its impact on correlation can be understood through theoretical models. The importance of experimental studies in this field, which provide insights into the behavior of quantum systems under confinement and pave the way for future applications in quantum technology is also emphasized.     

Entropy Generation during Head-On Interaction of Premixed Flames with Inert Walls within Turbulent Boundary Layers

The statistical behaviours of different entropy generation mechanisms in the head-on interaction of turbulent premixed flames with a chemically inert wall within turbulent boundary layers have been analysed using Direct Numerical Simulation data. The entropy generation characteristics in the case of head-on premixed flame interaction with an isothermal wall is compared to that for an adiabatic wall. It has been found that entropy generation due to chemical reaction, thermal diffusion and molecular mixing remain comparable when the flame is away from the wall for both wall boundary conditions. However, the wall boundary condition affects the entropy generation during flame-wall interaction. In the case of isothermal wall, the entropy generation due to chemical reaction vanishes because of flame quenching and the entropy generation due to thermal diffusion becomes the leading entropy generator at the wall. By contrast, the entropy generation due to thermal diffusion and molecular mixing decrease at the adiabatic wall because of the vanishing wall-normal components of the gradients of temperature and species mass/mole fractions. These differences have significant effects on the overall entropy generation rate during flame-wall interaction, which suggest that combustor wall cooling needs to be optimized from the point of view of structural integrity and thermodynamic irreversibility.     

Application of Advanced Synchrotron Radiation–Based and Conventional Molecular Techniques in Recent Research on Molecular Structure,Metabolic Characteristics,and Nutrition in Coproducts from Biofuel Processing

Abstract

Advanced synchrotron radiation infrared microspectroscopy, as a nondestructive and rapid analytical technique, is able to simultaneously reveal the structural, chemical, and environmental features of biomaterials at cellular and molecular levels within intact tissue. However, to date, this advanced synchrotron-based technique is still seldom used by feed and nutrition scientists. This article aims to provide detailed information regarding how to apply advanced synchrotron radiation–based and conventional molecular techniques to research in coproducts from biofuel processing on the molecular structure, metabolic characteristics, and nutrition. The information described in this article provides better insight on coproduct research progress and updates with advanced synchrotron radiation-based and globar-based (conventional) molecular spectroscopy.     

Information‐theoretic chemometric analyses of Raman data for chemical reaction studies

A methodology of multivariate chemometric techniques based on the information‐theoretic approach was applied for elucidating chemical reaction information from a Raman data array R _m×ν that arises from in situ reaction monitoring. This reaction‐induced dynamic dataset R _m×ν can be contaminated by random cosmic ray spikes found in the midst of characteristic spectral variations associated with the disappearance or emergence of Raman active reactants, intermediates and products. Such spurious cosmic spikes were identified and removed using a novel and fast numerical approach based on maximum and minimum spectral entropy principles while preserving the genuine reaction‐induced spectral variations. Subsequently, the band‐target entropy minimization (BTEM) algorithm, a minimum spectral entropy based self‐modeling curve resolution technique, was applied to recover the pure component spectra of Raman active chemical species. Information gain through the chemometric analyses was calculated using information entropies with base 2 logarithm. This sequence of information‐theoretic chemometric analyses (or transinformations) was successfully tested on the reaction spectral data obtained from alcoholysis of acetic anhydride, which contains four Raman active chemical species. It is envisioned that this series of multivariate statistical analyses will be useful in chemical reaction studies and process analytical technology (PAT) applications that utilize in situ Raman spectroscopy to monitor transient dynamic changes in chemical concentrations, and also in Raman microscopy/imaging data containing spatial variations. Copyright © 2010 John Wiley & Sons, Ltd.     

The statistical mechanics of particles obeying discrete spatial quantum theory

The energy levels for a particle confined to a one dimensional potential well are calculated using discrete spatial QM. The partition function is constructed and approximations are made to evaluate it thus generating an expression for the energy, entropy and chemical potential of an ensemble of such particles. The concept of negative temperature is applied to the above system and applications to the early universe are also discussed.     

结构声强技术测量墙体结构中弯曲波耦合功率流

虽然结构声强技术已成功地应用于匀质薄壁结构，但在建筑结构的应用研究只是一些定性的探讨，本文应用结构声强技术研究建筑结构中弯曲波声强的测量，以传统方法获得的结构总损耗能量测量值为参考，基于９５％合成置信区间研究弯曲波声强的测量精度，初步探讨了结构声强技术在建筑中应用的可行性。     

Entropy-Based Behavioural Efficiency of the Financial Market

The most known and used abstract model of the financial market is based on the concept of the informational efficiency (EMH) of that market. The paper proposes an alternative which could be named the behavioural efficiency of the financial market, which is based on the behavioural entropy instead of the informational entropy. More specifically, the paper supports the idea that, in the financial market, the only measure (if any) of the entropy is the available behaviours indicated by the implicit information. Therefore, the behavioural entropy is linked to the concept of behavioural efficiency. The paper argues that, in fact, in the financial markets, there is not a (real) informational efficiency, but there exists a behavioural efficiency instead. The proposal is based both on a new typology of information in the financial market (which provides the concept of implicit information—that is, that information ”translated” by the economic agents from observing the actual behaviours) and on a non-linear (more exactly, a logistic) curve linking the behavioural entropy to the behavioural efficiency of the financial markets. Finally, the paper proposes a synergic overcoming of both EMH and AMH based on the new concept of behavioural entropy in the financial market.     

Electrochemical tip-enhanced Raman Spectroscopy for microscopic studies of electrochemical interfaces

The review describes electrochemical applications of tip-enhanced Raman spectroscopy (TERS). These applications combine the merits of both scanning probe microscopy (SPM) and Raman spectroscopy, which enables us to simultaneously obtain high-resolution images of surface morphology and chemical information under the electrochemical environment. This review, first summarizes the pioneering work done on the TERS systems that operate in liquid and electrochemical environments, and then gives an overview of the typical instrumentation of electrochemical TERS (EC-TERS) based on electrochemical scanning tunneling microscopy (EC-STM). Furthermore, this review summarizes the advancements in EC-TERS studies of events that occur at the interfaces. These include potential dependent structural changes and electrochemical reactions. Finally, we discuss the current issues and future prospects of EC-TERS for microscopic studies of electrochemical interfaces.     

熔体局部结构的分子动力学模拟研究

计算机技术的迅速发展使分子动力学模拟成为可能。这是一种直接方法用以更详细地了解液态的结构。文章介绍在分子动力学模拟产生的一系列平衡瞬态构型基础上的等近邻键序参数方法和使用这一方法对若干熔体局部结构的研究，包括若干碱金属卤化物熔盐，ＣａＦ２快离子态和熔融态，熔融态ＺｎＣｌ２和Ｒｂ２ＺｎＣｌ４，ＢＢＯ熔体和晶体生长母液等。     

Macroscopic Time Evolution and MaxEnt Inference for Closed Systems with Hamiltonian Dynamics

MaxEnt inference algorithm and information theory are relevant for the time evolution of macroscopic systems considered as problem of incomplete information. Two different MaxEnt approaches are introduced in this work, both applied to prediction of time evolution for closed Hamiltonian systems. The first one is based on Liouville equation for the conditional probability distribution, introduced as a strict microscopic constraint on time evolution in phase space. The conditional probability distribution is defined for the set of microstates associated with the set of phase space paths determined by solutions of Hamilton’s equations. The MaxEnt inference algorithm with Shannon’s concept of the conditional information entropy is then applied to prediction, consistently with this strict microscopic constraint on time evolution in phase space. The second approach is based on the same concepts, with a difference that Liouville equation for the conditional probability distribution is introduced as a macroscopic constraint given by a phase space average. We consider the incomplete nature of our information about microscopic dynamics in a rational way that is consistent with Jaynes’ formulation of predictive statistical mechanics, and the concept of macroscopic reproducibility for time dependent processes. Maximization of the conditional information entropy subject to this macroscopic constraint leads to a loss of correlation between the initial phase space paths and final microstates. Information entropy is the theoretic upper bound on the conditional information entropy, with the upper bound attained only in case of the complete loss of correlation. In this alternative approach to prediction of macroscopic time evolution, maximization of the conditional information entropy is equivalent to the loss of statistical correlation, and leads to corresponding loss of information. In accordance with the original idea of Jaynes, irreversibility appears as a consequence of gradual loss of information about possible microstates of the system.     

The Odyssey of Entropy: Cryptography

After being introduced by Shannon as a measure of disorder and unavailable information, the notion of entropy has found its applications in a broad range of scientific disciplines. In this paper, we present a systematic review on the applications of entropy and related information-theoretical concepts in the design, implementation and evaluation of cryptographic schemes, algorithms, devices and systems. Moreover, we study existing trends, and establish a roadmap for future research in these areas.     

Cheminformatics analysis and learning in a data pipelining environment

Summary Workflow technology is being increasingly applied in discovery information to organize and analyze data. SciTegic's Pipeline Pilot is a chemically intelligent implementation of a workflow technology known as data pipelining. It allows scientists to construct and execute workflows using components that encapsulate many cheminformatics based algorithms. In this paper we review SciTegic's methodology for molecular fingerprints, molecular similarity, molecular clustering, maximal common subgraph search and Bayesian learning. Case studies are described showing the application of these methods to the analysis of discovery data such as chemical series and high throughput screening results. The paper demonstrates that the methods are well suited to a wide variety of tasks such as building and applying predictive models of screening data, identifying molecules for lead optimization and the organization of molecules into families with structural commonality.     

REDAN: relative entropy-based dynamical allosteric network model

ABSTRACT

Protein allostery is ubiquitous phenomena that are important for cellular signalling processes. Despite extensive methodology development, a quantitative model is still needed to accurately measure protein allosteric response upon external perturbation. Here, we introduced the relative entropy concept from information theory as a quantitative metric to develop a method for measurement of the population shift with regard to protein structure during allosteric transition. This method is referred to as relative entropy-based dynamical allosteric network (REDAN) model. Using this method, protein allostery could be evaluated at three mutually dependent structural levels: allosteric residues, allosteric pathways, and allosteric communities. All three levels are carried out using rigorous searching algorithms based on relative entropy. Application of the REDAN model on the second PDZ domain (PDZ2) in the human PTP1E protein provided metric-based insight into its allostery upon peptide binding.     

The Relevance of Interactions in Nanoparticle Systems – Application to Particulate Thin Films

In the field of Particle Technology, processes cannot yet be designed from basic molecular understanding. Nanotechnology, however, begins to bridge this gap between molecules and particles and may thus open up new ways not only for the production and handling of particulate matter but also for the engineered design of advanced material properties. The visions and applications in nanoparticle technology cover a broad range, for instance quantum dots in information technology, refractory particles for advanced ceramics, highly active substances in pharmacy, catalysts or micro‐ and mesoporous adsorbents, to name only a few applications. Starting from the concept of product engineering, we investigate the basic preconditions for tailoring nanoparticulate properties, i.e. the control of the particle interactions. This concept is then applied to particulate thin film formation as an example of structure formation. The structure of dip‐coated samples, defined as the order of particles within the layer, was found to vary with the pH and the ion concentration adjusted in the sol bath. It was observed that the surface roughness scanned by an atomic force microscope increased with increasing electrolyte concentration. The structural evolution of the particulate network was studied by measuring the viscosity as a function of shear rate and solid concentration. Finally, the influence of coating structures on the transmission properties was determined. Especially in the case of LaCl₃ a strong dependence was observed. The results explicitly confirm a correlation between microscopic structure and macroscopic properties.     

Can experiments select the configurational component of excess entropy?

Configurational entropy is frequently used to rationalize the structural dynamics of glass-forming liquids. The main problem with this concept is that it is not directly accessible to experiments. We introduce a procedure to estimate the configurational component of the excess entropy of a liquid --specifically, the configurational-entropy contribution from the structural relaxation process-- through a combined investigation of dynamic and thermodynamic properties as functions of temperature and pressure. We test our method on orthoterphenyl, salol, and glycerol, and find that the fraction of excess entropy that arises from structural configurations is about 70% for all three materials.Received: 29 April 2004, Published online: 29 June 2004PACS: 64.70.Pf Glass transitions - 78.35. + c Brillouin and Rayleigh scattering; other light scattering - 77.22.Gm Dielectric loss and relaxation     

Tight-binding molecular dynamics study of the hydrogen-induced structural modifications in tetrahedral amorphous carbon

A tight-binding molecular dynamics study of the structural evolution in tetrahedral amorphous carbon networks under dynamic hydrogen saturation is presented. The incorporation of hydrogen results in higher degrees of network disorder in second-neighbour distances, and initiates orbital re-hybridization that relaxes network stress. Using the simulated structures, numerical tests are performed to verify the effectiveness of a new structural order parameter for tetrahedrally-bonded solids. It is found that the island of accessible information, within the order parameter field shows a linear dependence between the fluctuations in first- and second-nearest-neighbour distances at a preferred orientation of 36°. A comparison with similar studies on hydrogenated amorphous silicon suggests that the local network structure of tetrahedrally-bonded amorphous solids obey the same ordering rule irrespective of differences in chemical species.