Numerical simulation and pattern characterization of nonlinear spatiotemporal dynamics on fractal surfaces for the whole-heart modeling applications

Engineered and natural systems often involve irregular and self-similar geometric forms,which is called fractal geometry. For instance, precision machining produces a visuallyflat surface, while which looks like a rough mountain in the nanometer scale under themicroscope. Human heart consists of a fractal network of muscle cells, Purkinje fibers,arteries and veins. Cardiac electrical activity exhibits highly nonlinear and fractalbehaviors. Although space-time dynamics occur on the fractal geometry, e.g., chemicaletching on the surface of machined parts and electrical conduction in the heart, most ofexisting works modeled space-time dynamics (e.g., reaction, diffusion and propagation) onthe Euclidean geometry (e.g., flat planes and rectangular volumes). This brings inaccurateapproximation of real-world dynamics, due to sensitive dependence of nonlinear dynamicalsystems on initial conditions. In this paper, we developed novel methods and tools for thenumerical simulation and pattern recognition of spatiotemporal dynamics on fractalsurfaces of complex systems, which include (1) characterization and modeling of fractalgeometry, (2) fractal-based simulation and modeling of spatiotemporal dynamics, (3)recognizing and quantifying spatiotemporal patterns. Experimental results show that theproposed methods outperform traditional modeling approaches based on the Euclideangeometry, and provide effective tools to model and characterize space-time dynamics onfractal surfaces of complex systems.     

Surface-enhanced raman scattering and nonlinear optics applied to electrochemistry

The most recently developed diagnostic technique in metal-electrolyte and metal-gas interfaces adapts spontaneous Raman scattering and nonlinear optical generation, techniques normally applied to bulk media, to surface science investigation. For certain metallic surfaces, an enormous increase exists in the Raman (as much as 10⁶ to 10⁸ times) and nonlinear optical signals resulting from submonolayer coverage of molecular adsorbates at the interface. Spontaneous Raman scattering and nonlinear optical scattering are well developed in both theory and practice for the analysis of molecular structure and concentration in bulk media. Instrumentation to generate and detect these inelastically scattered signals is readily available and is adequate for adaption to surface science. However, the mechanism (or mechanisms) giving rise to such a large enhancement at the interfaces is still being actively researched and remains controversial. Theoretical and experimental investigations related to the underlying physics of this enhancement and the application of such surface enhancement as a vibrational probe for adsorbates on the metal surface have been labeled “surface-enhanced Raman scattering” (SERS) and “surface-enhanced nonlinear optics”. Soon after the recognition that molecules adsorbed onto metal electrodes under certain conditions exhibit an anomalously large Raman scattering efficiency,^1–3 it became evident that such a phenomenon makes possible an in situ diagnostic probe for detailed and unique vibrational signatures of adsorbates in the ambient phase (electrolyte and atmospheric gas surroundings). Optical spectroscopy in the visible range has a much higher energy resolution (e.g., 0. I cm-I) than is presently available in electron energy loss spectroscopy (EELS), as well as the capability to measure much lower frequency modes (e.g., as low as 5 cm^?1) than is possible in infrared spectroscopy. Perhaps the most significant attribute of SERS and surface-enhanced nonlinear optical scattering is that the surrounding media in front of the interface (e.g., several meters of gas and several centimeters of liquid) do not introduce optical loss or overwhelmingly large signals. The recognition that SERS is capable of performing vibrational spectroscopy with this resolution, frequency range, and in such dense surroundings has therefore brought an explosion of activity to the field since 1977.     

On the possibility of study the surface structure of small bio-objects, including fragments of nucleotide chains, by means of electron interference

We propose a new method to study the surface of small bio-objects, including macromolecules and their complexes. This method is based on interference of low-energy electrons. Theoretically, this type of interference may allow to construct a hologram of the biological object, but, unlike an optical hologram, with the spatial resolution of the order of inter-atomic distances. The method provides a possibility to construct a series of such holograms at various levels of electron energies. In theory, obtaining such information would be enough to identify the types of molecular groups existing on the surface of the studied object. This method could also be used for “fast reading” of nucleotide chains. It has been shown how to depose a long linear molecule as a straight line on a substrate before carrying out such “reading”.     

Unified Green's function retrieval by cross correlation

It has been shown by many authors that the cross correlation of two recordings of a diffuse wave field at different receivers yields the Green's function between these receivers. Recently the theory has been extended for situations where time-reversal invariance does not hold (e.g., in attenuating media) and where source-receiver reciprocity breaks down (in moving fluids). Here we present a unified theory for Green's function retrieval that captures all these situations and, because of the unified form, readily extends to more complex situations, such as electrokinetic Green's function retrieval in poroelastic or piezoelectric media. The unified theory has a wide range of applications in "remote sensing without a source."     

A Unified Treatment of Tribo-Components Degradation Using Thermodynamics Framework: A Review on Adhesive Wear

An extensive survey of open literature reveals the need for a unifying approach for characterizing the degradation of tribo-pairs. This paper focuses on recent efforts made towards developing unified relationships for adhesive-type wear under unlubricated conditions through a thermodynamic framework. It is shown that this framework can properly characterize many complex scenarios, such as degradation problems involving unidirectional, bidirectional (oscillatory and reciprocating motions), transient operating conditions (e.g., during the running-in period), and variable loading/speed sequencing.     

The Molecular Design of Fluorescent Sensors for Ionic Analytes

Molecular fluorescent sensors can be synthesized by covalently linking a photoactive fragment (e.g., anthracene) to a receptor subunit displaying affinity toward the envisaged substrate. The electron transfer process is the privileged signal transduction mechanism: redox active substrates (e.g., transition metals) typically release/uptake an electron to/from the proximate photoexcited fluorophore, the recognition being signaled through fluorescence quenching; redox inactive substrates (d⁰ and d¹⁰ metals, H⁺) deactivate an existing quenching relay (e.g., a tertiary nitrogen atom close to the fluorophore) and their recognition is signaled through fluorescence enhancement. An-ionic substrates can be conveniently recognized on the basis of the metal–ligand interaction: polyamine receptors containing the photophysically inactive Zn^IIion bind the carboxylate group. In the case of amino acids, , selectivity is improved when the receptor platform bears additional groups capable to interact specifically with the R substituent. If R is capable of transferring an electron to the nearby photoexcited fluorophore, the recognition is signaled through fluorescence quenching.     

Doping and Surface Modification of Carbon Quantum Dots for Enhanced Functionalities and Related Applications

Carbon quantum dots (CQDs) are a unique class of 0D nanomaterials, featured by a graphitic core and shell layers saturated with hydrogen atoms and functional groups. CQDs are prepared through top-down and bottom-up strategies from natural and synthetic precursors. CQDs can be modified through chemical (e.g., surface functionalization/passivation, doping, etc.) and physical (e.g., core–shell architecture, composite material blending, etc.) strategies to control their properties. This review highlights the effect of such modifications on the photophysical properties of CQDs, such as photoluminescence (PL), absorbance, and relaxivity. The dependence of PL upon the size, orientation at the edges, surface and edge functionalization, doping, excitation wavelength, concentration, pH, aggregate formation, etc., are summarized along with the supporting theoretical evidence available in the literature. Also, this review outlines the recent advancements, and future prospective of optical (e.g., sensing, bioimaging, and fluorescent ink) and catalytic applications (e.g., photocatalysis and electrocatalysis) of CQDs enhanced through physical and chemical modifications of their structure and composition.     

Consistent Quantification of Complex Dynamics via a Novel Statistical Complexity Measure

Natural systems often show complex dynamics. The quantification of such complex dynamics is an important step in, e.g., characterization and classification of different systems or to investigate the effect of an external perturbation on the dynamics. Promising routes were followed in the past using concepts based on (Shannon’s) entropy. Here, we propose a new, conceptually sound measure that can be pragmatically computed, in contrast to pure theoretical concepts based on, e.g., Kolmogorov complexity. We illustrate the applicability using a toy example with a control parameter and go on to the molecular evolution of the HIV1 protease for which drug treatment can be regarded as an external perturbation that changes the complexity of its molecular evolutionary dynamics. In fact, our method identifies exactly those residues which are known to bind the drug molecules by their noticeable signal. We furthermore apply our method in a completely different domain, namely foreign exchange rates, and find convincing results as well.     

Electron impact ionization of thymine clusters embedded in superfluid helium droplets

Embedding molecules in helium clusters has become a powerful technique for the preparation of cold targets for spectroscopy experiments, as well as for the assembly of complex, fragile molecular species. We have recently developed a helium cluster source and a pick-up cell to produce neutral beams of doped helium droplets, to be used as targets in studies on electron collisions with molecules of biological relevance. In the present work we present the results of a series of experiments on electron-impact ionization of helium clusters doped with thymine and 1-methylthymine, where several interesting phenomena were observed, i.e., (i) electron impact ionization of molecular clusters inside the helium droplets leads predominantly to protonated clusters; (ii) the appearance energies are close to the ionization threshold of the helium atom but ionization efficiency curves in addition extend down by several eV; (iii) ionized molecular clusters can undergo metastable decay via the loss of one neutral monomer.     

Linguistic contributions to speech-on-speech masking for native and non-native listeners: language familiarity and semantic content

This study examined whether speech-on-speech masking is sensitive to variation in the degree of similarity between the target and the masker speech. Three experiments investigated whether speech-in-speech recognition varies across different background speech languages (English vs Dutch) for both English and Dutch targets, as well as across variation in the semantic content of the background speech (meaningful vs semantically anomalous sentences), and across variation in listener status vis-a?-vis the target and masker languages (native, non-native, or unfamiliar). The results showed that the more similar the target speech is to the masker speech (e.g., same vs different language, same vs different levels of semantic content), the greater the interference on speech recognition accuracy. Moreover, the listener's knowledge of the target and the background language modulate the size of the release from masking. These factors had an especially strong effect on masking effectiveness in highly unfavorable listening conditions. Overall this research provided evidence that that the degree of target-masker similarity plays a significant role in speech-in-speech recognition. The results also give insight into how listeners assign their resources differently depending on whether they are listening to their first or second language.     

Isotope fractionation by thermal diffusion in silicate melts

Isotopes fractionate in thermal gradients, but there is little quantitative understanding of this effect in complex fluids. Here we present results of experiments and molecular dynamics simulations on silicate melts. We show that isotope fractionation arises from classical mechanical effects, and that a scaling relation based on Chapman-Enskog theory predicts the behavior seen in complex fluids without arbitrary fitting parameters. The scaling analysis reveals that network forming elements (Si and O) fractionate significantly less than network modifiers (e.g., Mg, Ca, Fe, Sr, Hf, and U).     

Comparative analysis of heterogeneous solid and soft materials by adsorption, NMR and thermally stimulated depolarisation current methods

Structural characterisation of such bio-objects as fibrinogen solution, yeast cells, wheat seeds and bone tissues has been done using two versions of cryoporometry based on the integral Gibbs-Thomson (IGT) equation for freezing point depression of pore liquids and the measurements by ¹H NMR spectroscopy (180-200 < T < 273 K) and the thermally stimulated depolarisation current (TSDC) method (90 < T < 273 K) of structured water. The IGT equation was solved using a self-consisting regularization procedure including the maximum entropy principle applied to the distribution function of pore size (PSD). Both methods give clear pictures of changes in the structural characteristics caused, e.g., by hydration and swelling of wheat seeds and yeast cells, coagulation and interaction of fibrinogen with solid nanoparticles in the aqueous media, and the human bone tissue disease.     

Molecular dynamics study of contact mechanics: contact area and interfacial separation from small to full contact

We report a molecular dynamics study of the contact between a rigid solid with a randomly rough surface and an elastic block with a flat surface. We study the contact area and the interfacial separation from small contact (low load) to full contact (high load). For small load the contact area varies linearly with the load and the interfacial separation depends logarithmically on the load. For high load the contact area approaches the nominal contact area (i.e., complete contact), and the interfacial separation approaches zero. The present results may be very important for soft solids, e.g., rubber, or for very smooth surfaces, where complete contact can be reached at moderate high loads without plastic deformation of the solids.     

Amphifunctional Mesoporous Silica Nanoparticles with “Molecular Gates” for Controlled Drug Uptake and Release

It is demonstrated that the uptake and release of hydrophobic drugs/dyes by mesoporous silica nanoparticles (MSN) is critically dependent on the functional groups present on their outer surfaces. For this, amphifunctional MSNs are synthesized, possessing hydrophobic pores and hydrophilic functional groups on the outer surface. Further, the outer surface is modified with a different chain length of molecules, e.g., propargyl alcohol, triethylene glycol, and PEG (2000) via azide–alkyne click chemistry. The effect of these different surface functional groups on uptake of drug/dye is demonstrated with Nile red, proflavine (free base form), and rhodamine 6G. The uptake of these molecules is found to be inversely proportional to the bulkiness of surface functionality. To counter this effect, an alternate method of loading is proposed and demonstrated. Finally, the effect of these different functional groups on the release of loaded drug proflavine is studied, which supports the hypothesis that bulkier outer surface groups also hinder the release of drugs loaded in the porous MSN.     

Simple three-parameter model potential for diatomic systems: from weakly and strongly bound molecules to metastable molecular ions

Based on a simplest molecular-orbital theory of H(2)(+), a three-parameter model potential function is proposed to describe ground-state diatomic systems with closed-shell and/or S-type valence-shell constituents over a significantly wide range of internuclear distances. More than 200 weakly and strongly bound diatomics have been studied, including neutral and singly charged diatomics (e.g., H(2), Li(2), LiH, Cd(2), Na(2)(+), and RbH(-)), long-range bound diatomics (e.g., NaAr, CdNe, He(2), CaHe, SrHe, and BaHe), metastable molecular dications (e.g., BeH(++), AlH(++), Mg(2)(++), and LiBa(++)), and molecular trications (e.g., YHe(+++) and ScHe(+++)).     

Conditions for noncollinear instabilities of ferromagnetic materials

Two criteria have been identified here which determine whether a magnetic metal orders in a collinear (e.g., ferromagnet) or noncollinear (e.g., spin-spiral) arrangement. These criteria involve the ratio between the strength of the exchange interaction and the width of the electron bands, as well as Fermi-surface nesting between spin-up and spin-down sheets of the Fermi surface. Based on our analysis we predict that even typical ferromagnetic materials (e.g., Fe, Co, and Ni) should be possible to stabilize in a noncollinear magnetic order in, e.g., high pressure experiments.     

Dynamical screening and ionic conductivity in water from ab initio simulations

We present a method to calculate ionic conductivities of complex fluids from ab initio simulations. This is achieved by combining density functional theory molecular dynamics simulations with polarization theory. Conductivities are then obtained via a Green-Kubo formula using time-dependent effective charges of electronically screened ions. The method is applied to two different phases of warm dense water. We observe large fluctuations in the effective charges; protons can transport effective charges greater than +e for ultrashort time scales. Furthermore, we compare our results with a simpler model of ionic conductivity in water that is based on diffusion coefficients. Our approach can be directly applied to study ionic conductivities of electronically insulating materials of arbitrary composition, e.g., complex molecular mixtures under such extreme conditions that occur deep inside giant planets.     

Planarization process of single crystalline silicon asperity under abrasive rolling effect studied by molecular dynamics simulation

In the chemical mechanical polishing (CMP) process, the complex behaviors of abrasive particles play important roles in the planarization of wafer surface. Particles embedded in the pad remove materials by ploughing, while particles immersed in the slurry by rolling across the wafer surface. In this paper, processes of the particle rolling across a silicon surface with an asperity under various down forces and external driving forces were studied using molecular dynamics (MD) simulation method. The simulations clarified the asperity shape evolution during the rolling process and analyzed the energy changes of the simulation system and the interaction forces acted on the silica particle. It was shown that both the down force and the driving force had important influences on the amount of the material removed. With relatively small down forces and driving forces applied on the particle, the material removal occurred mainly in the front end of the asperity; when the down forces and driving forces were large enough, e.g., 100?nN, the material removal could take place at the whole top part of the asperity. The analysis of energy changes and interaction forces provided favorable explanations to the simulation results.     

Factors influencing recognition of interrupted speech

This study examined the effect of interruption parameters (e.g., interruption rate, on-duration and proportion), linguistic factors, and other general factors, on the recognition of interrupted consonant-vowel-consonant (CVC) words in quiet. Sixty-two young adults with normal-hearing were randomly assigned to one of three test groups, "male65," "female65" and "male85," that differed in talker (male/female) and presentation level (65/85 dB SPL), with about 20 subjects per group. A total of 13 stimulus conditions, representing different interruption patterns within the words (i.e., various combinations of three interruption parameters), in combination with two values (easy and hard) of lexical difficulty were examined (i.e., 13×2=26 test conditions) within each group. Results showed that, overall, the proportion of speech and lexical difficulty had major effects on the integration and recognition of interrupted CVC words, while the other variables had small effects. Interactions between interruption parameters and linguistic factors were observed: to reach the same degree of word-recognition performance, less acoustic information was required for lexically easy words than hard words. Implications of the findings of the current study for models of the temporal integration of speech are discussed.