Bridging large and small scales of water models using hybrid Molecular Dynamics/Fluctuating Hydrodynamics framework

This thesis presents a two-dimensional water model investigation and development of a multiscale method for the modelling of large systems, such as virus in water or peptide immersed in the solvent. We have implemented a two-dimensional ‘Mercedes Benz’ (MB) or BN2D water model using Molecular Dynamics. We have studied its dynamical and structural properties dependence on the model’s parameters. For the first time we derived formulas to calculate thermodynamic properties of the MB model in the microcanonical (NVE) ensemble. We also derived equations of motion in the isothermal–isobaric (NPT) ensemble. We have analysed the rotational degree of freedom of the model in both ensembles. We have developed and implemented a self-consistent multiscale method, which is able to communicate micro- and macro- scales. This multiscale method assumes, that matter consists of the two phases. One phase is related to micro- and the other to macroscale. We simulate the macro scale using Landau Lifshitz-Fluctuating Hydrodynamics, while we describe the microscale using Molecular Dynamics. We have demonstrated that the communication between the disparate scales is possible without introduction of fictitious interface or approximations which reduce the accuracy of the information exchange between the scales. We have investigated control parameters, which were introduced to control the contribution of each phases to the matter behaviour. We have shown, that microscales inherit dynamical properties of the macroscales and vice versa, depending on the concentration of each phase. We have shown, that Radial Distribution Function is not altered and velocity autocorrelation functions are gradually transformed, from Molecular Dynamics to Fluctuating Hydrodynamics description, when phase balance is changed. In this work we test our multiscale method for the liquid argon, BN2D and SPC/E water models. For the SPC/E water model we investigate microscale fluctuations which are computed using advanced mapping technique of the small scales to the large scales, which was developed by Voulgarakisand et. al.

Novel neuronal and astrocytic mechanisms in thalamocortical loop dynamics

In this review, we summarize three sets of findings that have recently been observed in thalamic astrocytes and neurons, and discuss their significance for thalamocortical loop dynamics. (i) A physiologically relevant ‘window’ component of the low–voltage–activated, T–type Ca2+ current (ITwindow) plays an essential part in the slow (less than 1 Hz) sleep oscillation in adult thalamocortical (TC) neurons, indicating that the expression of this fundamental sleep rhythm in these neurons is not a simple reflection of cortical network activity. It is also likely that ITwindow underlies one of the cellular mechanisms enabling TC neurons to produce burst firing in response to novel sensory stimuli. (ii) Both electrophysiological and dye–injection experiments support the existence of gap junction–mediated coupling among young and adult TC neurons. This finding indicates that electrical coupling–mediated synchronization might be implicated in the high and low frequency oscillatory activities expressed by this type of thalamic neuron. (iii) Spontaneous intracellular Ca2+ ([Ca2+]i) waves propagating among thalamic astrocytes are able to elicit large and long–lasting N–methyl–D–aspartate–mediated currents in TC neurons. The peculiar developmental profile within the first two postnatal weeks of these astrocytic [Ca2+]i transients and the selective activation of these glutamate receptors point to a role for this astrocyte–to–neuron signalling mechanism in the topographic wiring of the thalamocortical loop. As some of these novel cellular and intracellular properties are not restricted to thalamic astrocytes and neurons, their significance may well apply to (patho)physiological functions of glial and neuronal elements in other brain areas.

Distances between Predicates in By-Analogy Reasoning Systems

The purpose is to develop expert systems where by-analogy reasoning is used. Knowledge “closeness” problems are known to frequently emerge in such systems if knowledge is represented by different production rules. To determine a degree of closeness for production rules a distance between predicates is introduced. Different types of distances between two predicate value distribution functions are considered when predicates are “true”. Asymptotic features and interrelations of distances are studied. Predicate value distribution functions are found by empirical distribution functions, and a procedure is proposed for this purpose. An adequacy of obtained distribution functions is tested on the basis of the statistical 2 χ –criterion and a testing mechanism is discussed. A theorem, by which a simple procedure of measurement of Euclidean distances between distribution function parameters is substituted for a predicate closeness determination one, is proved for parametric distribution function families. The proposed distance measurement apparatus may be applied in expert systems when reasoning is created by analogy.

Leveraging Existing Plasma Simulation Codes

This paper describes the process of wrapping existing scientific codes in the domain of plasma physics simulations through the use of the Sun’s Java Native Interface. We have created a Java front-end for a particular functionality, offered by legacy native libraries, in order to achieve reusability and interoperability without having to rewrite these libraries. The technique, introduced in this paper, includes two approaches – the one-to-one mapping for wrapping a number of native functions, and using peer classes for wrapping native data structures.

On Li’s Coefficients for Some Classes of L-Functions

AMS Subj. Classification: 11M41, 11M26, 11S40

Differential effectiveness of two anxiety induction procedures in youth and older adult populations

In this study, we tested in older and younger adults the efficacy of two well-known procedures to experimentally induce anxiety: a) Velten self-statements combined with music; b) film scenes. We extended the pre-vious findings in this field to the understudied area of mood induction in older adults. Fifty-seven older adults and 94 college students were random-ly assigned to one of the experimental conditions or to a control group. Results indicated that both procedures were effective, according to a series of ANOVAs for several self-report, physiological, and behavioral measures. Likewise, the highest effect sizes were observed for the Velten procedure (g = .81 vs. g = .71), and the effects were significantly higher in younger (g = 1.0 in the Velten condition) than in older adults (g = .62), Q = 4.25, X2(1), p = .0392. Both procedures were effective to induce inducting anxiety in both age groups, especially the Velten procedure in younger adults. Therefore, Velten self-statements combined with music may be very useful anxiety induction procedure for further research in controlled situa-tions of emotions across the life-span.

Target/error overlap in jargonaphasia:the case for a one-source model, lexical and non-lexical summation, and the special status of correct responses

We present three jargonaphasic patients who made phonological errors in naming, repetition and reading. We analyse target/response overlap using statistical models to answer three questions: 1) Is there a single phonological source for errors or two sources, one for target-related errors and a separate source for abstruse errors? 2) Can correct responses be predicted by the same distribution used to predict errors or do they show a completion boost (CB)? 3) Is non-lexical and lexical information summed during reading and repetition? The answers were clear. 1) Abstruse errors did not require a separate distribution created by failure to access word forms. Abstruse and target-related errors were the endpoints of a single overlap distribution. 2) Correct responses required a special factor, e.g., a CB or lexical/phonological feedback, to preserve their integrity. 3) Reading and repetition required separate lexical and non-lexical contributions that were combined at output.

The value of magnetoencephalography to guide electrode implantation in epilepsy

Purpose: To investigate if magnetoencephalography (MEG) can identify implantation sites for intracranial recordings (IR). Method: Two groups of 12 patients assessed for surgery with IR with and without MEG were compared (MEG and control groups). In the control group, non-invasive presurgical assessment without MEG suggested clear hypotheses for implantation. In the MEG group, non-invasive assessment was inconclusive, and MEG was used to identify implantation sites. Both groups were matched for implantation type. The success of implantation was defined by findings in IR: a) Focal seizure onset; b)Unilateral focal abnormal responses to single pulse electrical stimulation(SPES); and c) Concordance between a) and b). Results: In all MEG patients, at least one virtual MEG electrode generated suitable hypotheses for the location of implantations. The proportion of patients showing focal seizure onset restricted to one hemisphere was similar in control and MEG groups (6/12 vs. 11/12, Fisher’s exact test,p = 0.0686). The proportion of patients showing unilateral responses to SPES was lower in the control than in the MEG group (7/12 vs. 12/12,p = 0.0373). Conclusion: The MEG group showed similar or higher incidence of successful implantations than controls.

Resonance properties of domain boundaries in quasi-two dimensional antiferromagnets

The so-called "internal modes" localized near the domain boundaries in quasi-two dimensional antiferromagnets are investigated. The possible localized states are classified and their frequency dependences on the system discreteness parameter λ=J/β, which describes the ratio of the magnitudes of the exchange interplane interaction and the magnetic anisotropy, are found. A sudden change in the spectrum of the local internal modes is observed at a critical value of this parameter, λ=λb=3/4, where the domain wall shifts from a collinear to a canted shape. When λ<λb there are one symmetric and two antisymmetric local modes, and when λ>λb the modes are two symmetric, one antisymmetric, and one shear. For discreteness parameters close to the critical value, the frequencies of some of the local modes lie deep inside the gap for the linear AFM magnon spectrum and can be observed experimentally. © 2010 American Institute of Physics.

Investigating the ability of antibodies to recognize specific oxidized protein epitopes

There is a growing awareness that inflammatory diseases have an oxidative pathology, which can result in specific oxidation of amino acids within proteins. Antibody-based techniques for detecting oxidative posttranslational modifications (oxPTMs) are often used to identify the level of protein oxidation. There are many commercially available antibodies but some uncertainty to the potential level of cross reactivity they exhibit; moreover little information regarding the specific target epitopes is available. The aim of this work was to investigate the potential of antibodies to distinguish between select peptides with and without oxPTMs. Two peptides, one containing chlorotyrosine (DY-Cl-EDQQKQLC) and the other an unmodified tyrosine (DYEDQQKQLC) were synthesized and complementary anti-sera were produced in sheep using standard procedures. The anti-sera were tested using a half-sandwich ELISA and the anti-serum raised against the chloro-tyrosine containing peptide showed increased binding to the chlorinated peptide, whereas the control anti-serum bound similarly to both peptides. This suggested that antibodies can discriminate between similar peptide sequences with and without an oxidative modification. A peptide (STSYGTGC) and its variants with chlorotyrosine or nitrotyrosine were produced. The anti-sera showed substantially less binding to these alternative peptides than to the original peptides the anti-sera were produced against. Work is ongoing to test commercially available antibodies against the synthetic peptides as a comparison to the anti-sera produced in sheep. In conclusion, the antisera were able to distinguish between oxidatively modified and unmodified peptides, and two different sequences around the modification site.

The exploration enhancement workshop: An exploration-based approach to facilitating identity formation in young adults

This dissertation reports an investigation of the utility of two intervention programs to facilitate identity formation by way of exploration, one designed from an explicitly self-construction point of view and the other designed from an explicitly self-discovery point of view. The self-construction program was implemented using cognitive skills and orientations derived from Berzonsky (1989), Grotevant (1987), and Kurtines (1999). The self-discovery program was implemented using affective insight development strategies derived from Csikszentmihalyi (1990), Maslow (1968), and Waterman (1990). Three sets of measures were used: (a) cognitive identity measures, (b) affective identity measures, and (c) overall identity measures. Ninety undergraduates from Florida International University completed the intervention. Participants were assigned to one of three intervention conditions (Cognitive, Affective, and Control) and were pretested and posttested on cognitive, affective, and overall identity measures. Intervention strategies were introduced and discussed in the context of specific goals and choices that participants brought to group. Intervention results were then analyzed in terms of the effectiveness of the intervention conditions in promoting their respective developmental domains. The intervention was effective in promoting identity development in comparison to the control condition, with the cognitive condition facilitating cognitive competence and the affective condition facilitating affective insight. Results are discussed in the context of the constructivist and discovery perspectives, as well as in light of the broadened view of exploration offered in this paper. ^

Customization of the design of antenna using genetic algorithm and finite-difference time-domain technique

Antenna design is an iterative process in which structures are analyzed and changed to comply with certain performance parameters required. The classic approach starts with analyzing a "known" structure, obtaining the value of its performance parameter and changing this structure until the "target" value is achieved. This process relies on having an initial structure, which follows some known or "intuitive" patterns already familiar to the designer. The purpose of this research was to develop a method of designing UWB antennas. What is new in this proposal is that the design process is reversed: the designer will start with the target performance parameter and obtain a structure as the result of the design process. This method provided a new way to replicate and optimize existing performance parameters. The base of the method was the use of a Genetic Algorithm (GA) adapted to the format of the chromosome that will be evaluated by the Electromagnetic (EM) solver. For the electromagnetic study we used XFDTD™ program, based in the Finite-Difference Time-Domain technique. The programming portion of the method was created under the MatLab environment, which serves as the interface for converting chromosomes, file formats and transferring of data between the XFDTD™ and GA. A high level of customization had to be written into the code to work with the specific files generated by the XFDTD™ program. Two types of cost functions were evaluated; the first one seeking broadband performance within the UWB band, and the second one searching for curve replication of a reference geometry. The performance of the method was evaluated considering the speed provided by the computer resources used. Balance between accuracy, data file size and speed of execution was achieved by defining parameters in the GA code as well as changing the internal parameters of the XFDTD™ projects. The results showed that the GA produced geometries that were analyzed by the XFDTD™ program and changed following the search criteria until reaching the target value of the cost function. Results also showed how the parameters can change the search criteria and influence the running of the code to provide a variety of geometries.

Macroinvertebrate community response to eutrophication in an oligotrophic wetland: An in situ mesocosm experiment

Eutrophication from anthropogenic nutrient enrichment is a primary threat to the oligotrophic freshwater marshes of southern Florida. Macrophyte and periphyton response to increased phosphorus (P) has been well documented in both correlative and experimental studies, but the response of consumer communities remains poorly understood, especially in southern marl prairies. We conducted a P-loading experiment in in situ mesocosms in Taylor Slough, Everglades National Park, and examined the response of macroinvertebrate communities. Mesocosms at two sites were loaded weekly with P at four levels: control (0 g P/m2/yr), low (0.2 g P/m2/yr), intermediate (0.8 g P/m2/yr), and high (3.2 g P/m2/ yr). After ∼2 yrs of P-loading, macroinvertebrates were sampled using periphyton mat and benthic floc cores. Densities of macroinvertebrate taxa (no./g AFDM) were two to 16 times higher in periphyton mats than benthic floc. Periphyton biomass decreased with enrichment at one site, and periphyton was absent from many intermediate and all high P treatments at both sites. Total macroinvertebrate density in periphyton mats increased with intermediate P loads, driven primarily by chironomids and nematodes. Conversely, total macroinvertebrate density in benthic floc decreased with enrichment, driven primarily by loss of chironomids and ceratopogonids (Dasyhelea). This study suggests that macroinvertebrate density increases with enrichment until periphyton mats are lost, after which it decreases, and mat infauna fail to move into benthic substrates in response to mat loss. These results were noted at nutrient levels too low to yield anoxia, and we believe that the decrease of macroinvertebrate density resulted from a loss of habitat. This work illustrates the importance of periphyton mats as habitat for macroinvertebrates in the Everglades. This study also indicates that in this system, macroinvertebrate sampling should be designed to target periphyton mats or conducted with special attention to inclusion of substrates relative to their coverage.

A Q-Methodology approach to investigating the relationship between level of reflection and typologies among prospective teachers in the physics learning assistant program at Florida International University

The purpose of this mixed methods study was to understand physics Learning Assistants' (LAs) views on reflective teaching, expertise in teaching, and LA program teaching experience and to determine if views predicted level of reflection evident in writing. Interviews were conducted in Phase One, Q methodology was used in Phase Two, and level of reflection in participants' writing was assessed using a rubric based on Hatton and Smith's (1995) "Criteria for the Recognition of Evidence for Different Types of Reflective Writing" in Phase Three. Interview analysis revealed varying perspectives on content knowledge, pedagogical knowledge, and experience in relation to expertise in teaching. Participants revealed that they engaged in reflection on their teaching, believed reflection helps teachers improve, and found peer reflection beneficial. Participants believed teaching experience in the LA program provided preparation for teaching, but that more preparation was needed to teach. Three typologies emerged in Phase Two. Type One LAs found participation in the LA program rewarding and believed expertise in teaching does not require expertise in content or pedagogy, but it develops over time from reflection. Type Two LAs valued reflection, but not writing reflections, felt the LA program teaching experience helped them decide on non-teaching careers and helped them confront gaps in their physics knowledge. Type Three LAs valued reflection, believed expertise in content and pedagogy are necessary for expert teaching, and felt LA program teaching experience increased their likelihood of becoming teachers, but did not prepare them for teaching. Writing assignments submitted in Phase Three were categorized as 19% descriptive writing, 60% descriptive reflections, and 21% dialogic reflections. No assignments were categorized as critical reflection. Using ordinal logistic regression, typologies that emerged in Phase Two were not found to be predictors for the level of reflection evident in the writing assignments. In conclusion, viewpoints of physics LAs were revealed, typologies among them were discovered, and their writing gave evidence of their ability to reflect on teaching. These findings may benefit faculty and staff in the LA program by helping them better understand the views of physics LAs and how to assess their various forms of reflection.

A heuristic algorithm to generate test program sequences for moving probe electronic test equipment

The electronics industry, is experiencing two trends one of which is the drive towards miniaturization of electronic products. The in-circuit testing predominantly used for continuity testing of printed circuit boards (PCB) can no longer meet the demands of smaller size circuits. This has lead to the development of moving probe testing equipment. Moving Probe Test opens up the opportunity to test PCBs where the test points are on a small pitch (distance between points). However, since the test uses probes that move sequentially to perform the test, the total test time is much greater than traditional in-circuit test. While significant effort has concentrated on the equipment design and development, little work has examined algorithms for efficient test sequencing. The test sequence has the greatest impact on total test time, which will determine the production cycle time of the product. Minimizing total test time is a NP-hard problem similar to the traveling salesman problem, except with two traveling salesmen that must coordinate their movements. The main goal of this thesis was to develop a heuristic algorithm to minimize the Flying Probe test time and evaluate the algorithm against a "Nearest Neighbor" algorithm. The algorithm was implemented with Visual Basic and MS Access database. The algorithm was evaluated with actual PCB test data taken from Industry. A statistical analysis with 95% C.C. was performed to test the hypothesis that the proposed algorithm finds a sequence which has a total test time less than the total test time found by the "Nearest Neighbor" approach. Findings demonstrated that the proposed heuristic algorithm reduces the total test time of the test and, therefore, production cycle time can be reduced through proper sequencing.