5 resultados para BIOSPECIFIC INTERACTION ANALYSIS

em Bucknell University Digital Commons - Pensilvania - USA


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In an accelerated exclusion process (AEP), each particle can "hop" to its adjacent site if empty as well as "kick" the frontmost particle when joining a cluster of size ℓ⩽ℓ_{max}. With various choices of the interaction range, ℓ_{max}, we find that the steady state of AEP can be found in a homogeneous phase with augmented currents (AC) or a segregated phase with holes moving at unit velocity (UV). Here we present a detailed study on the emergence of the novel phases, from two perspectives: the AEP and a mass transport process (MTP). In the latter picture, the system in the UV phase is composed of a condensate in coexistence with a fluid, while the transition from AC to UV can be regarded as condensation. Using Monte Carlo simulations, exact results for special cases, and analytic methods in a mean field approach (within the MTP), we focus on steady state currents and cluster sizes. Excellent agreement between data and theory is found, providing an insightful picture for understanding this model system.

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As lightweight and slender structural elements are more frequently used in the design, large scale structures become more flexible and susceptible to excessive vibrations. To ensure the functionality of the structure, dynamic properties of the occupied structure need to be estimated during the design phase. Traditional analysis method models occupants simply as an additional mass; however, research has shown that human occupants could be better modeled as an additional degree-of- freedom. In the United Kingdom, active and passive crowd models are proposed by the Joint Working Group as a result of a series of analytical and experimental research. It is expected that the crowd models would yield a more accurate estimation to the dynamic response of the occupied structure. However, experimental testing recently conducted through a graduate student project at Bucknell University indicated that the proposed passive crowd model might be inaccurate in representing the impact on the structure from the occupants. The objective of this study is to provide an assessment of the validity of the crowd models proposed by JWG through comparing the dynamic properties obtained from experimental testing data and analytical modeling results. The experimental data used in this study was collected by Firman in 2010. The analytical results were obtained by performing a time-history analysis on a finite element model of the occupied structure. The crowd models were created based on the recommendations from the JWG combined with the physical properties of the occupants during the experimental study. During this study, SAP2000 was used to create the finite element models and to implement the analysis; Matlab and ME¿scope were used to obtain the dynamic properties of the structure through processing the time-history analysis results from SAP2000. The result of this study indicates that the active crowd model could quite accurately represent the impact on the structure from occupants standing with bent knees while the passive crowd model could not properly simulate the dynamic response of the structure when occupants were standing straight or sitting on the structure. Future work related to this study involves improving the passive crowd model and evaluating the crowd models with full-scale structure models and operating data.

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Vibration serviceability is a widely recognized design criterion for assembly-type structures, such as stadiums, that are likely subjected to rhythmic human-induced excitation. Human-induced excitation of a structure occurs from the movement of the occupants such as walking, running, jumping, or dancing. Vibration serviceability is based on the level of comfort that people have with the vibrations of a structure. Current design guidance uses the natural frequency of the structure to assess vibration serviceability. However, a phenomenon known as human-structure interaction suggests that there is a dynamic interaction between the structure and passive occupants, altering the natural frequency of the system. Human-structure interaction is dependent on many factors, including the dynamic properties of the structure, posture of the occupants, and relative size of the crowd. It is unknown if the shift in natural frequency due to humanstructure interaction is significant enough to warrant consideration in the design process. This study explores the interface of both structural and crowd characteristics through experimental testing to determine if human-structure interaction should be considered because of its potential impact on serviceability assessment. An experimental test structure that represents the dynamic properties of a cantilevered stadium structure was designed and constructed. Experimental modal analysis was implemented to determine the dynamic properties of the empty test structure and when occupied with up to seven people arranged in different locations and postures. Comparisons of the dynamic properties were made between the empty and occupied testing configurations and analytical results from the use of a dynamic crowd model recommended from the Joint Working Group of Europe. Data trends lead to the development of a refined dynamic crowd model. This dynamic model can be used in conjunction with a finite element model of the test structure to estimate the dynamic influence due to human-structure interaction due to occupants standing with straight knees. In the future, the crowd model will be refined and can aid in assessing the dynamic properties of in-service stadium structures.

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Collision-induced dissociation (CID) of peptides using tandem mass spectrometry (MS) has been used to determine the identity of peptides and other large biological molecules. Mass spectrometry (MS) is a useful tool for determining the identity of molecules based on their interaction with electromagnetic fields. If coupled with another method like infrared (IR) vibrational spectroscopy, MS can provide structural information, but in its own right, MS can only provide the mass-to-charge (m/z) ratio of the fragments produced, which may not be enough information to determine the mechanism of the collision-induced dissociation (CID) of the molecule. In this case, theoretical calculations provide a useful companion for MS data and yield clues about the energetics of the dissociation. In this study, negative ion electrospray tandem MS was used to study the CID of the deprotonated dipeptide glycine-serine (Gly-Ser). Though negative ion MS is not as popular a choice as positive ion MS, studies by Bowie et al. show that it yields unique clues about molecular structure which complement positive ion spectroscopy, such as characteristic fragmentations like the loss of formaldehyde from the serine residue.2 The increase in the collision energy in the mass spectrometer alters the flexibility of the dipeptide backbone, enabling isomerizations (reactions not resulting in a fragment loss) and dissociations to take place. The mechanism of the CID of Gly-Ser was studied using two computational methods, B3LYP/6-311+G* and M06-2X/6-311++G**. The main pathway for molecular dissociation was analyzed in 5 conformers in an attempt to verify the initial mechanism proposed by Dr. James Swan after examination of the MS data. The results suggest that the loss of formaldehyde from serine, which Bowie et al. indicates is a characteristic of the presence of serine in a protein residue, is an endothermic reaction that is made possible by the conversion of the translational energy of the ion into internal energy as the ion collides with the inert collision gas. It has also been determined that the M06-2X functional¿s improved description of medium and long-range correlation makes it more effective than the B3LYP functional at finding elusive transition states. M06-2X also more accurately predicts the energy of those transition states than does B3LYP. A second CID mechanism, which passes through intermediates with the same m/z ratio as the main pathway for molecular dissociation, but different structures, including a diketopiperazine intermediate, was also studied. This pathway for molecular dissociation was analyzed with 3 conformers and the M06-2X functional, due to its previously determined effectiveness. The results suggest that the latter pathway, which meets the same intermediate masses as the first mechanism, is lower in overall energy and therefore a more likely pathway of dissociation than the first mechanism.

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The effects of human-structure interaction on the dynamic performance of occupied structures have long been observed. The inclusion of the effects of human-structure interaction is important to ensure that the dynamic response of a structure is not overestimated. Previous observations, both in service and in the laboratory, have yielded results indicating that the effects are dependent on the natural frequency of the structure, the posture of the occupants, and the mass ratio of the occupants to the structure. These results are noteworthy, but are limited in their application,because the data are sparse and are only pertinent to a specific set of characteristics identified in a given study. To examine these characteristics simultaneously and consistently, an experimental test structure was designed with variable properties to replicate a variety of configurations within a controlled setting focusing on the effects of passive occupants. Experimental modal analysis techniques were employed to both the empty and occupied conditions of the structure and the dynamic properties associated with each condition were compared. Results similar to previous investigations were observed, including both an increase and a decrease in natural frequency of the occupied structure with respect to the empty structure, as well as the identification of a second mode of vibration. The damping of the combined system was higher for all configurations. Overall, this study provides a broad data set representing a wide array of configurations. The experimental results of this study were used to assess current recommendations for the dynamic properties of a crowd to analytically predict the effects of human-structure interaction. The experimental results were used to select a set of properties for passive, standing occupants and develop a new model that can more accurately represent the behavior of the human-structure system as experimentally measured in this study.