ASU Scholarship Showcase

Human protein diversity arises as a result of alternative splicing, single nucleotide polymorphisms (SNPs) and posttranslational modifications. Because of these processes, each protein can exists as multiple variants in vivo. Tailored strategies are needed to study these protein variants and understand their role in health and disease. In this work we utilized quantitative mass spectrometric immunoassays to determine the protein variants concentration of beta-2-microglobulin, cystatin C, retinol binding protein, and transthyretin, in a population of 500 healthy individuals. Additionally, we determined the longitudinal concentration changes for the protein variants from four individuals over a 6 month period. Along with the native forms of the four proteins, 13 posttranslationally modified variants and 7 SNP-derived variants were detected and their concentration determined. Correlations of the variants concentration with geographical origin, gender, and age of the individuals were also examined. This work represents an important step toward building a catalog of protein variants concentrations and examining their longitudinal changes.

Vision and Change in Undergraduate Biology Education outlined five core concepts intended to guide undergraduate biology education: 1) evolution; 2) structure and function; 3) information flow, exchange, and storage; 4) pathways and transformations of energy and matter; and 5) systems. We have taken these general recommendations and created a Vision and Change BioCore Guide—a set of general principles and specific statements that expand upon the core concepts, creating a framework that biology departments can use to align with the goals of Vision and Change. We used a grassroots approach to generate the BioCore Guide, beginning with faculty ideas as the basis for an iterative process that incorporated feedback from more than 240 biologists and biology educators at a diverse range of academic institutions throughout the United States. The final validation step in this process demonstrated strong national consensus, with more than 90% of respondents agreeing with the importance and scientific accuracy of the statements. It is our hope that the BioCore Guide will serve as an agent of change for biology departments as we move toward transforming undergraduate biology education.

The relation between flux and fluctuation is fundamental to complex physical systems that support and transport flows. A recently obtained law predicts monotonous enhancement of fluctuation as the average flux is increased, which in principle is valid but only for large systems. For realistic complex systems of small sizes, this law breaks down when both the average flux and fluctuation become large. Here we demonstrate the failure of this law in small systems using real data and model complex networked systems, derive analytically a modified flux-fluctuation law, and validate it through computations of a large number of complex networked systems. Our law is more general in that its predictions agree with numerics and it reduces naturally to the previous law in the limit of large system size, leading to new insights into the flow dynamics in small-size complex systems with significant implications for the statistical and scaling behaviors of small systems, a topic of great recent interest.

An outstanding and fundamental problem in contemporary physics is to include and probe the many-body effect in the study of relativistic quantum manifestations of classical chaos. We address this problem using graphene systems described by the Hubbard Hamiltonian in the setting of resonant tunneling. Such a system consists of two symmetric potential wells separated by a potential barrier, and the geometric shape of the whole domain can be chosen to generate integrable or chaotic dynamics in the classical limit. Employing a standard mean-field approach to calculating a large number of eigenenergies and eigenstates, we uncover a class of localized states with near-zero tunneling in the integrable systems. These states are not the edge states typically seen in graphene systems, and as such they are the consequence of many-body interactions. The physical origin of the non-edge-state type of localized states can be understood by the one-dimensional relativistic quantum tunneling dynamics through the solutions of the Dirac equation with appropriate boundary conditions. We demonstrate that, when the geometry of the system is modified to one with chaos, the localized states are effectively removed, implying that in realistic situations where many-body interactions are present, classical chaos is capable of facilitating greatly quantum tunneling. This result, besides its fundamental importance, can be useful for the development of nanoscale devices such as graphene-based resonant-tunneling diodes.

Dynamical systems based on the minority game (MG) have been a paradigm for gaining significant insights into a variety of social and biological behaviors. Recently, a grouping phenomenon has been unveiled in MG systems of multiple resources (strategies) in which the strategies spontaneously break into an even number of groups, each exhibiting an identical oscillation pattern in the attendance of game players. Here we report our finding of spontaneous breakup of resources into three groups, each exhibiting period-three oscillations. An analysis is developed to understand the emergence of the striking phenomenon of triple grouping and period-three oscillations. In the presence of random disturbances, the triple-group/period-three state becomes transient, and we obtain explicit formula for the average transient lifetime using two methods of approximation. Our finding indicates that, period-three oscillation, regarded as one of the most fundamental behaviors in smooth nonlinear dynamical systems, can also occur in much more complex, evolutionary-game dynamical systems. Our result also provides a plausible insight for the occurrence of triple grouping observed, for example, in the U.S. housing market.

Understanding the dynamics of human movements is key to issues of significant current interest such as behavioral prediction, recommendation, and control of epidemic spreading. We collect and analyze big data sets of human movements in both cyberspace (through browsing of websites) and physical space (through mobile towers) and find a superlinear scaling relation between the mean frequency of visit〈f〉and its fluctuation σ : σ ∼〈f⟩^β with β ≈ 1.2. The probability distribution of the visiting frequency is found to be a stretched exponential function. We develop a model incorporating two essential ingredients, preferential return and exploration, and show that these are necessary for generating the scaling relation extracted from real data. A striking finding is that human movements in cyberspace and physical space are strongly correlated, indicating a distinctive behavioral identifying characteristic and implying that the behaviors in one space can be used to predict those in the other.

The U.S. scientific research community does not reflect America's diversity. Hispanics, African Americans, and Native Americans made up 31% of the general population in 2010, but they represented only 18 and 7% of science, technology, engineering, and mathematics (STEM) bachelor's and doctoral degrees, respectively, and 6% of STEM faculty members (National Science Foundation [NSF], 2013). Equity in the scientific research community is important for a variety of reasons; a diverse community of researchers can minimize the negative influence of bias in scientific reasoning, because people from different backgrounds approach a problem from different perspectives and can raise awareness regarding biases (Intemann, 2009). Additionally, by failing to be attentive to equity, we may exclude some of the best and brightest scientific minds and limit the pool of possible scientists (Intemann, 2009). Given this need for equity, how can our scientific research community become more inclusive?

The phenomenon of Fano resonance is ubiquitous in a large variety of wave scattering systems, where the resonance profile is typically asymmetric. Whether the parameter characterizing the asymmetry should be complex or real is an issue of great experimental interest. Using coherent quantum transport as a paradigm and taking into account of the collective contribution from all available scattering channels, we derive a universal formula for the Fano-resonance profile. We show that our formula bridges naturally the traditional Fano formulas with complex and real asymmetry parameters, indicating that the two types of formulas are fundamentally equivalent (except for an offset). The connection also reveals a clear footprint for the conductance resonance during a dephasing process. Therefore, the emergence of complex asymmetric parameter when fitting with experimental data needs to be properly interpreted. Furthermore, we have provided a theory for the width of the resonance, which relates explicitly the width to the degree of localization of the close-by eigenstates and the corresponding coupling matrices or the self-energies caused by the leads. Our work not only resolves the issue about the nature of the asymmetry parameter, but also provides deeper physical insights into the origin of Fano resonance. Since the only assumption in our treatment is that the transport can be described by the Green’s function formalism, our results are also valid for broad disciplines including scattering problems of electromagnetic waves, acoustics, and seismology.

Persistent currents (PCs), one of the most intriguing manifestations of the Aharonov-Bohm (AB) effect, are known to vanish for Schrödinger particles in the presence of random scatterings, e.g., due to classical chaos. But would this still be the case for Dirac fermions? Addressing this question is of significant value due to the tremendous recent interest in two-dimensional Dirac materials. We investigate relativistic quantum AB rings threaded by a magnetic flux and find that PCs are extremely robust. Even for highly asymmetric rings that host fully developed classical chaos, the amplitudes of PCs are of the same order of magnitude as those for integrable rings, henceforth the term superpersistent currents (SPCs). A striking finding is that the SPCs can be attributed to a robust type of relativistic quantum states, i.e., Dirac whispering gallery modes (WGMs) that carry large angular momenta and travel along the boundaries. We propose an experimental scheme using topological insulators to observe and characterize Dirac WGMs and SPCs, and speculate that these features can potentially be the base for a new class of relativistic qubit systems. Our discovery of WGMs in relativistic quantum systems is remarkable because, although WGMs are common in photonic systems, they are relatively rare in electronic systems.

Background: Healthy individuals on the lower end of the insulin sensitivity spectrum also have a reduced gene expression response to exercise for specific genes. The goal of this study was to determine the relationship between insulin sensitivity and exercise-induced gene expression in an unbiased, global manner.

Methods and Findings: Euglycemic clamps were used to measure insulin sensitivity and muscle biopsies were done at rest and 30 minutes after a single acute exercise bout in 14 healthy participants. Changes in mRNA expression were assessed using microarrays, and miRNA analysis was performed in a subset of 6 of the participants using sequencing techniques. Following exercise, 215 mRNAs were changed at the probe level (Bonferroni-corrected P<0.00000115). Pathway and Gene Ontology analysis showed enrichment in MAP kinase signaling, transcriptional regulation and DNA binding. Changes in several transcription factor mRNAs were correlated with insulin sensitivity, including MYC, r=0.71; SNF1LK, r=0.69; and ATF3, r= 0.61 (5 corrected for false discovery rate). Enrichment in the 5’-UTRs of exercise-responsive genes suggested regulation by common transcription factors, especially EGR1. miRNA species of interest that changed after exercise included miR-378, which is located in an intron of the PPARGC1B gene.

Conclusions: These results indicate that transcription factor gene expression responses to exercise depend highly on insulin sensitivity in healthy people. The overall pattern suggests a coordinated cycle by which exercise and insulin sensitivity regulate gene expression in muscle.