Drag Prediction Using Adaptive Discontinuous Finite Elements

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/106502/1/AIAA2013-51.pd

A mixed‐studies systematic review of the experiences of body image, disordered eating, and eating disorders during the COVID‐19 pandemic

Objectives: This systematic review assessed the influence of the COVID-19 pan-demic and associated restrictions on body image, disordered eating (DE), and eating disorder outcomes. Methods: After registration on PROSPERO, a search was conducted for papers published between December 1, 2019 and August 1, 2021, using the databases Psy-cINFO, PsycARTICLES, CINAHL Plus, AMED, MEDLINE, ERIC, EMBASE, Wiley, and ProQuest (dissertations and theses).Results: Data from 75 qualitative, quantitative, and mixed-methods studies were synthesized using a convergent integrated approach and presented narratively within four themes: (1) disruptions due to the COVID-19 pandemic; (2) variability in the improvement or exacerbation of symptoms; (3) factors associated with body image and DE outcomes; (4) unique challenges for marginalized and under represented groups. Disruptions due to the pandemic included social and functional restrictions. Although most studies reported a worsening of concerns, some participants also reported symptom improvement or no change as a result of the pandemic. Factors associated with worse outcomes included psychological, individual, social, and eating disorder-related variables. Individuals identifying as LGBTQ+reported unique concerns during COVID-19. Discussion: There is large variability in individuals' responses to COVID-19 and limited research exploring the effect of the pandemic on body image, DE, and eating dis-order outcomes using longitudinal and experimental study designs. In addition, further research is required to investigate the effect of the COVID-19 pandemic onbody image and eating concerns among minoritized, racialized, underrepresented, or otherwise marginalized participants. Based on the findings of this review, we make recommendations for individuals, researchers, clinicians, and public health messaging. Public Significance: This review of 75 studies highlights the widespread negative impacts that the COVID-19 pandemic and associated restrictions have had on body image and disordered eating outcomes. It also identifies considerable variations in both the improvement and exacerbation of said outcomes that individuals, researchers, clinicians, and other public health professionals should be mindful of if we are to ensure that vulnerable people get the tailored support they require

Statistical mechanics of RNA folding: a lattice approach

We propose a lattice model for RNA based on a self-interacting two-tolerant trail. Self-avoidance and elements of tertiary structure are taken into account. We investigate a simple version of the model in which the native state of RNA consists of just one hairpin. Using exact arguments and Monte Carlo simulations we determine the phase diagram for this case. We show that the denaturation transition is first order and can either occur directly or through an intermediate molten phase.Comment: 8 pages, 9 figure

Statistical mechanics of secondary structures formed by random RNA sequences

The formation of secondary structures by a random RNA sequence is studied as a model system for the sequence-structure problem omnipresent in biopolymers. Several toy energy models are introduced to allow detailed analytical and numerical studies. First, a two-replica calculation is performed. By mapping the two-replica problem to the denaturation of a single homogeneous RNA in 6-dimensional embedding space, we show that sequence disorder is perturbatively irrelevant, i.e., an RNA molecule with weak sequence disorder is in a molten phase where many secondary structures with comparable total energy coexist. A numerical study of various models at high temperature reproduces behaviors characteristic of the molten phase. On the other hand, a scaling argument based on the extremal statistics of rare regions can be constructed to show that the low temperature phase is unstable to sequence disorder. We performed a detailed numerical study of the low temperature phase using the droplet theory as a guide, and characterized the statistics of large-scale, low-energy excitations of the secondary structures from the ground state structure. We find the excitation energy to grow very slowly (i.e., logarithmically) with the length scale of the excitation, suggesting the existence of a marginal glass phase. The transition between the low temperature glass phase and the high temperature molten phase is also characterized numerically. It is revealed by a change in the coefficient of the logarithmic excitation energy, from being disorder dominated to entropy dominated.Comment: 24 pages, 16 figure

Single-molecule experiments in biological physics: methods and applications

I review single-molecule experiments (SME) in biological physics. Recent technological developments have provided the tools to design and build scientific instruments of high enough sensitivity and precision to manipulate and visualize individual molecules and measure microscopic forces. Using SME it is possible to: manipulate molecules one at a time and measure distributions describing molecular properties; characterize the kinetics of biomolecular reactions and; detect molecular intermediates. SME provide the additional information about thermodynamics and kinetics of biomolecular processes. This complements information obtained in traditional bulk assays. In SME it is also possible to measure small energies and detect large Brownian deviations in biomolecular reactions, thereby offering new methods and systems to scrutinize the basic foundations of statistical mechanics. This review is written at a very introductory level emphasizing the importance of SME to scientists interested in knowing the common playground of ideas and the interdisciplinary topics accessible by these techniques. The review discusses SME from an experimental perspective, first exposing the most common experimental methodologies and later presenting various molecular systems where such techniques have been applied. I briefly discuss experimental techniques such as atomic-force microscopy (AFM), laser optical tweezers (LOT), magnetic tweezers (MT), biomembrane force probe (BFP) and single-molecule fluorescence (SMF). I then present several applications of SME to the study of nucleic acids (DNA, RNA and DNA condensation), proteins (protein-protein interactions, protein folding and molecular motors). Finally, I discuss applications of SME to the study of the nonequilibrium thermodynamics of small systems and the experimental verification of fluctuation theorems. I conclude with a discussion of open questions and future perspectives.Comment: Latex, 60 pages, 12 figures, Topical Review for J. Phys. C (Cond. Matt

Single Molecule Statistics and the Polynucleotide Unzipping Transition

We present an extensive theoretical investigation of the mechanical unzipping of double-stranded DNA under the influence of an applied force. In the limit of long polymers, there is a thermodynamic unzipping transition at a critical force value of order 10 pN, with different critical behavior for homopolymers and for random heteropolymers. We extend results on the disorder-averaged behavior of DNA's with random sequences to the more experimentally accessible problem of unzipping a single DNA molecule. As the applied force approaches the critical value, the double-stranded DNA unravels in a series of discrete, sequence-dependent steps that allow it to reach successively deeper energy minima. Plots of extension versus force thus take the striking form of a series of plateaus separated by sharp jumps. Similar qualitative features should reappear in micromanipulation experiments on proteins and on folded RNA molecules. Despite their unusual form, the extension versus force curves for single molecules still reveal remnants of the disorder-averaged critical behavior. Above the transition, the dynamics of the unzipping fork is related to that of a particle diffusing in a random force field; anomalous, disorder-dominated behavior is expected until the applied force exceeds the critical value for unzipping by roughly 5 pN.Comment: 40 pages, 18 figure

Capturing the essence of folding and functions of biomolecules using Coarse-Grained Models

The distances over which biological molecules and their complexes can function range from a few nanometres, in the case of folded structures, to millimetres, for example during chromosome organization. Describing phenomena that cover such diverse length, and also time scales, requires models that capture the underlying physics for the particular length scale of interest. Theoretical ideas, in particular, concepts from polymer physics, have guided the development of coarse-grained models to study folding of DNA, RNA, and proteins. More recently, such models and their variants have been applied to the functions of biological nanomachines. Simulations using coarse-grained models are now poised to address a wide range of problems in biology.Comment: 37 pages, 8 figure