Bulletin of the American Physical Society
19th Annual Meeting of the APS Northwest Section
Volume 63, Number 6
Thursday–Saturday, May 31–June 2 2018; Tacoma, Washington
Session G2: Bio and Multidisciplinary Physics II |
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Chair: Andreas Vasdekis, University of Idaho Room: Thompson Hall 193 |
Saturday, June 2, 2018 3:30PM - 4:00PM |
G2.00001: Allostery through protein-induced DNA bubbles Invited Speaker: Nikolaos Voulgarakis The role of DNA is not limited only to carrying and protecting the genetic code. DNA may also play a very active role in its own functions. There is increasing experimental evidence that conformational and dynamic changes of the double strand may direct protein aggregations that are responsible for fundamental functions of DNA. Using a simple reaction-diffusion model, I will show that the coalescence of protein-induced DNA bubbles can mediate allosteric interactions that drive such protein aggregation. We will also discuss how this new type of allostery could regulate (a) the packaging of DNA and (b) the assembly of the transcription machinery.\\ \\In collaboration with: Traverso Joseph, Washington State University; Valipuram Manoranjan, Washington State University; Kim Rasmussen, Los Alamos National Laboratory; Alan Bishop, Los Alamos National Laboratory [Preview Abstract] |
Saturday, June 2, 2018 4:00PM - 4:12PM |
G2.00002: Predicting peak spectral sensitivities of vertebrate cone visual pigments using atomistic molecular simulations Jagdish Suresh Patel, Celeste Brown, F. Marty Ytreberg, Deborah Stenkamp Vertebrate visual perception is initiated when light strikes rod and cone photoreceptors within the retina of the eye. Peak spectral sensitivities ($\lambda_{\mathrm{max}})$ of visual pigments, are a function of the type of chromophore and the amino acid sequence of the associated opsin protein in the photoreceptors. To determine how minor sequence differences could result in large spectral shifts, we selected a spectrally-diverse group of 14 teleost Rh2 cone opsins for which sequences and $\lambda _{\mathrm{max\thinspace }}$are experimentally known. Molecular dynamics simulations were carried out after embedding cone opsin homology structures within explicit bilayers and water. Simulations revealed structural features of the chromophore, that contributed to diverged spectral sensitivities. Statistical tests performed on all the observed structural parameters of the chromophore revealed that a two-term, first-order regression model was sufficient to accurately predict $\lambda_{\mathrm{max\thinspace }}$(R$^{\mathrm{2}}$=$0.94)$ over a range of 452-528 nm. This approach was efficient and simple in that site-by-site molecular modifications were not required to predict $\lambda_{\mathrm{max}}$. [Preview Abstract] |
Saturday, June 2, 2018 4:12PM - 4:24PM |
G2.00003: The Influence of Free-Energy Surfaces on Mode-Dependent Protein Dynamics Eric Beyerle, Marina Guenza The analysis and description of protein motions is greatly facilitated by reducing the effective dimensionality of the system through coarse-graining and transforming to decoupled normal-mode coordinates. Principal-component analysis (PCA) is a popular method used to quantify and visualize the motions of proteins through a normal mode decomposition of an appropriate covariance matrix. However, its description of mode-dependent dynamics does not account for barriers on free-energy surfaces. We have found that the inclusion of free-energy barriers can influence the dynamics predicted by each mode. Here we compare the dynamics predicted by our method (the Langevin Equation for Protein Dynamics, LE4PD) and PCA. The comparison is facilitated by analytically mapping the bond-bond connectivity matrix used in the LE4PD onto the covariance matrix used in PCA. We find that the motions of PCA are restricted to specific regions of the free-energy surface and that they are not, in general, 'aware' of the most-probable energetic pathways present along each normal mode. A more detailed description of the dynamics represented by each mode is found by using the finite-temperature string method to find the most probable pathway along the free-energy surface. [Preview Abstract] |
Saturday, June 2, 2018 4:24PM - 4:36PM |
G2.00004: Abstract moved to D1.36 |
Saturday, June 2, 2018 4:36PM - 4:48PM |
G2.00005: Why living things cannot exist over 10 thousand years? Han Yongquan Einstein's theory of relativity holds that time stops when moving at the velocity of light. Suppose we move at the velocity of light. It can be understood that radiation (light velocity) exists and our life exists. The age of the life is the age of the universe---13.8 billion years. The exits of life on the planet, the larger the speed of rotation of the planet, the larger the age of its life. There is a limit age for the biological age on Earth, which is determined by the velocity of rotation of the earth. The earth's equator has a linear velocity of about 460 m/s, and the velocity of light is 3 x 10$^{\mathrm{8}}$ m/s. The age of the universe is 1.38 x 10$^{\mathrm{10}}$m/s. From this we can draw a ratio: 3 x 10$^{\mathrm{8}}$:460 $=$ 1.38 x 10$^{\mathrm{10}}$: x the value of x is the limit of the biological age of the earth. Calculate the value of x,x $=$ 2.12 × 10$^{\mathrm{4}}$ (years), this calculation results, not only meet the existing biological age limit of the earth, but also one of Einstein's theory of relativity verification and application. We can further speculate that if there is superluminal motion, it is possible and correct that time is back. [Preview Abstract] |
Saturday, June 2, 2018 4:48PM - 5:00PM |
G2.00006: High-throughput combitorial sputtering for metastable transition metal nitride alloys Bethany Matthews, Elisabetta Arca, Stephan Lany, Andriy Zakutayev, Janet Tate Sputtering is a high energy deposition technique that has many uses in industry and research and development. Recently it has been used in the high-throughput investigation of compositional variations in many material systems due to its ability to configure multiple material targets for co-sputtering at the same time. Additionally, new technologies in characterization tools allow for quick spatial mapping of these material libraries. Recently, new metastable ternary nitride structures have been predicted by theorists at the National Renewable Energy Laboratory and Lawrence Berkeley National Laboratory. Here we explore the system Zn$_{\mathrm{x}}$W$_{\mathrm{1-x}}$N, which is predicted to have a metastable wurtzite phase, which is different than the common antibixbyite (Zn$_{\mathrm{3}}$N$_{\mathrm{4}})$ and cubic (W$_{\mathrm{2}}$N). Structure and composition were mapped by x-ray diffraction and x-ray fluorescence spectroscopy respectively. The resistivity of various compositions was examined by four point probe. Optical transmission and reflection were measured to determine optical absorption for the various absorption. [Preview Abstract] |
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