Protein storytelling through physics.
Ontology highlight
ABSTRACT:
SUBMITTER: Brini E
PROVIDER: S-EPMC7945008 | biostudies-literature |
REPOSITORIES: biostudies-literature
Similar Datasets
Project description:Cancer is the leading cause of mortality among Alaska Native people. Over half of Alaska Native people live in rural communities where specially trained community members called Community Health Aides/Practitioners (CHA/Ps) provide health care. In response to CHA/Ps' expressed desire to learn more about cancer, four 5-day cancer education and digital storytelling courses were provided in 2014. Throughout each course, participants explored cancer information, reflected on their personal experiences, and envisioned how they might apply their knowledge within their communities. Each course participant also created a personal and authentic digital story, a methodology increasingly embraced by Indigenous communities as a way to combine storytelling traditions with modern technology to promote both individual and community health. Opportunities to learn of CHA/Ps' experiences with cancer and digital storytelling included a 3-page end-of-course written evaluation, a weekly story-showing log kept for 4 weeks post-course, a group teleconference held 1-2 weeks post-course, and a survey administered 6 months post-course. Participants described digital storytelling as a culturally respectful way to support cancer awareness and education. Participants described the process of creating digital stories as supporting knowledge acquisition, encouraging personal reflection, and sparking a desire to engage in cancer risk reduction activities for themselves and with their families and patients. As a result of creating a personalized digital story, CHA/Ps reported feeling differently about cancer, noting an increase in cancer knowledge and comfort to talk about cancer with clients and family. Indigenous digital stories have potential for broad use as a culturally appropriate health messaging tool.
| S-EPMC4943464 | biostudies-literature
Project description:The inverse protein folding problem, also known as protein sequence design, seeks to predict an amino acid sequence that folds into a specific structure and performs a specific function. Recent advancements in machine learning techniques have been successful in generating functional sequences, outperforming previous energy function-based methods. However, these machine learning methods are limited in their interoperability and robustness, especially when designing proteins that must function under non-ambient conditions, such as high temperature, extreme pH, or in various ionic solvents. To address this issue, we propose a new Physics-Informed Neural Networks (PINNs)-based protein sequence design approach. Our approach combines all-atom molecular dynamics simulations, a PINNs MD surrogate model, and a relaxation of binary programming to solve the protein design task while optimizing both energy and the structural stability of proteins. We demonstrate the effectiveness of our design framework in designing proteins that can function under non-ambient conditions.
| S-EPMC10046838 | biostudies-literature
Project description:Performative counter-storytelling can be a powerful experience for both the artists who create these stories and the audiences who witness them. This study examined audience responses to a counter-narrative (entitled "AMKA") performed by Africans in Australia which intended to present more complex, holistic, and strengths-based representations of their communities than those currently circulated by dominant discourses. Guided by a critical whiteness lens, the study explored how 34 self-identifying white audience members interpreted the performance and how they questioned whiteness by assuming the role of implicated witnesses. Following thematic analysis of mixed closed- and open-ended post-performance survey responses, audience members made connections between the content of AMKA and the contemporary political and cultural contexts in which it was performed and began to examine their positions of privilege and power. This study has provided evidence for the potential of political theater in creating spaces of encounter whereby responsible listening positions can be nurtured in the journey toward dismantling personal, and potentially structural, racially-based injustices.
| S-EPMC8672364 | biostudies-literature
Project description:This paper explores the abstraction of classical physics and applies several metrics that explore the evolution of social opinion. These metrics include an abstraction of Newtonian kinematics: mass, position, speed, acceleration, and Newtonian dynamics, an abstraction of force. Poll data is fit to a 2nd-order polynomial and a logistic function. These fits are used to understand the acceleration of opinion shift, and we explore recent social, cultural, and environmental trends, such as views on global climate change. We compare our results with the evolution of communication technologies and time spent on devices over the past 120 years. We show that the model connects the evolution in opinion with an abstraction of a Galilean concept: acceleration is independent of mass. Finally, we discuss the model of social polarization and the non-linear effect of media such as echo chambers.
| S-EPMC8971447 | biostudies-literature
Project description:The heavy fermion intermetallic compound URu2Si2 exhibits a hidden-order phase below the temperature of 17.5?K, which supports both anomalous metallic behavior and unconventional superconductivity. While these individual phenomena have been investigated in detail, it remains unclear how they are related to each other and to what extent uranium f-electron valence fluctuations influence each one. Here we use ligand site substituted URu2Si(2-x)P(x) to establish their evolution under electronic tuning. We find that while hidden order is monotonically suppressed and destroyed for x?0.035, the superconducting strength evolves non-monotonically with a maximum near x?0.01 and that superconductivity is destroyed near x?0.028. This behavior reveals that hidden order depends strongly on tuning outside of the U f-electron shells. It also suggests that while hidden order provides an environment for superconductivity and anomalous metallic behavior, it's fluctuations may not be solely responsible for their progression.
| S-EPMC4762885 | biostudies-other
Project description:Transmedia storytelling involves telling a story using multiple distinct media. The remit of stories that fall under this broad definition is vast, consequently causing theorists to examine different phenomena using tools that are not suitable for all forms of transmedia storytelling. The lack of critical tools means we are unable to describe, compare and analyse different experiences using common language. In this paper, we present our model that can be used to identify the fundamental structural features of a variety of transmedia storytelling forms. We illustrate its usage with twenty case studies and discuss how three groups of patterns emerge which can be identifiable in all transmedia stories. These patterns can be used to extend transmedia language and help form taxonomies, by identifying common patterns and their usages amongst various forms of transmedia stories.
| S-EPMC6993987 | biostudies-literature
Project description:The hypothesis that folding robustness is the primary determinant of the evolution rate of proteins is explored using a coarse-grained off-lattice model. The simplicity of the model allows rapid computation of the folding probability of a sequence to any folded conformation. For each robust folder, the network of sequences that share its native structure is identified. The fitness of a sequence is postulated to be a simple function of the number of misfolded molecules that have to be produced to reach a characteristic protein abundance. After fixation probabilities of mutants are computed under a simple population dynamics model, a Markov chain on the fold network is constructed, and the fold-averaged evolution rate is computed. The distribution of the logarithm of the evolution rates across distinct networks exhibits a peak with a long tail on the low rate side and resembles the universal empirical distribution of the evolutionary rates more closely than either distribution resembles the log-normal distribution. The results suggest that the universal distribution of the evolutionary rates of protein-coding genes is a direct consequence of the basic physics of protein folding.
| S-EPMC2840281 | biostudies-literature
Project description:Large, destructive earthquakes often propagate along thrust faults including megathrusts. The asymmetric interaction of thrust earthquake ruptures with the free surface leads to sudden variations in fault-normal stress, which affect fault friction. Here, we present full-field experimental measurements of displacements, particle velocities, and stresses that characterize the rupture interaction with the free surface, including the large normal stress reductions. We take advantage of these measurements to investigate the dependence of dynamic friction on transient changes in normal stress, demonstrate that the shear frictional resistance exhibits a significant lag in response to such normal stress variations, and identify a predictive frictional formulation that captures this effect. Properly accounting for this delay is important for simulations of fault slip, ground motion, and associated tsunami excitation.
| S-EPMC7474586 | biostudies-literature
Project description:Graphene is considered a record-performance nonlinear-optical material on the basis of numerous experiments. The observed strong nonlinear response ascribed to the refractive part of graphene's electronic third-order susceptibility ?(3) cannot, however, be explained using the relatively modest ?(3) value theoretically predicted for the 2D material. Here we solve this long-standing paradox and demonstrate that, rather than ?(3)-based refraction, a complex phenomenon which we call saturable photoexcited-carrier refraction is at the heart of nonlinear-optical interactions in graphene such as self-phase modulation. Saturable photoexcited-carrier refraction is found to enable self-phase modulation of picosecond optical pulses with exponential-like bandwidth growth along graphene-covered waveguides. Our theory allows explanation of these extraordinary experimental results both qualitatively and quantitatively. It also supports the graphene nonlinearities measured in previous self-phase modulation and self-(de)focusing (Z-scan) experiments. This work signifies a paradigm shift in the understanding of 2D-material nonlinearities and finally enables their full exploitation in next-generation nonlinear-optical devices.
| S-EPMC6041291 | biostudies-other
Project description:Physics-based potentials have been developed for the interactions between proteins and DNA for simulations with the UNRES + NARES-2P force field. The mean-field interactions between a protein and a DNA molecule can be divided into eight categories: (1) nonpolar side chain–DNA base, (2) polar uncharged side chain–DNA base, (3) charged side chain–DNA base, (4) peptide group–phosphate group, (5) peptide group–DNA base, (6) nonpolar side chain–phosphate group, (7) polar uncharged side chain–phosphate group, and (8) charged side chain–phosphate group. Umbrella-sampling molecular dynamics simulations in explicit TIP3P water using the AMBER force field were carried out to determine the potentials of mean force (PMF) for all 105 pairs of interacting components. Approximate analytical expressions for the mean-field interaction energy of each pair of the different kinds of interacting molecules were then fitted to the PMFs to obtain the parameters of the analytical expressions. These analytical expressions can reproduce satisfactorily the PMF curves corresponding to different orientations of the interacting molecules. The results suggest that the physics-based mean-field potentials of amino acid–nucleotide interactions presented here can be used in coarse-grained simulation of protein–DNA interactions.
| S-EPMC4455907 | biostudies-literature