Bulletin of the American Physical Society
2013 Annual Fall Meeting of the APS Prairie Section
Volume 58, Number 15
Thursday–Saturday, November 7–9, 2013; Columbia, Missouri
Session D2: Biological Physics |
Hide Abstracts |
Chair: Ioan Kosztin, University of Missouri Room: Memorial Union Stotler I&II |
Friday, November 8, 2013 2:00PM - 2:12PM |
D2.00001: Predictive modeling of the fusion of uneven multi-cellular aggregates using Cellular Particle Dynamics simulations Matthew McCune, Ashkan Shafiee, Gabor Forgacs, Ioan Kosztin Cellular Particle Dynamics (CPD) is an effective computational method for describing and predicting the time evolution of passive biomechanical relaxation processes of multi-cellular aggregates. A typical such relaxation process is the fusion of spheroidal bioink particles during post bioprinting structure formation. In CPD cells are modeled as an ensemble of cellular particles (CPs) that interact via short-range contact interactions, characterized by an attractive (adhesive interaction) and a repulsive (excluded volume interaction) component. The time evolution of the spatial conformation of the multicellular system is determined by following the trajectories of all CPs through integration of their equations of motion. CPD was successfully applied to describe and predict the fusion of 3D tissue construct involving identical spherical aggregates. Here, we demonstrate that CPD can also predict tissue formation involving uneven spherical aggregates whose volumes decreases during the fusion process. [Preview Abstract] |
Friday, November 8, 2013 2:12PM - 2:24PM |
D2.00002: Investigation of SHAPE mechanism with RNA 3D structure modeling Peinan Zhao, Travis Hurst, Xiaojun Xu, Kevin Weeks, Shijie Chen Selective 2$'$-hydroxyl acylation by primer extension (SHAPE) chemical probing method for RNA reflects local structural dynamics, which is intrinsically related to RNA three-dimensional structure. To gain quantitative insights into the relationship between RNA three-dimensional structure and SHAPE reactivity, we develop an algorithm to rebuild the SHAPE profile from the three-dimensional structure. The algorithm starts from RNA structures and combines nucleotide interaction strength and conformational flexibility, ligand (SHAPE reagent) accessibility and base-pairing pattern through a composite function. Comparisons between the predicted SHAPE profile and experimental SHAPE data show high correlation, suggesting the validity of the extracted analytical function. The validity of the theory supports the model for the key factors that determine SHAPE reactivity profile. Furthermore, the theory offers an effective method to select viable RNA three-dimensional structures from an ensemble of decoy structure models. [Preview Abstract] |
Friday, November 8, 2013 2:24PM - 2:36PM |
D2.00003: ABSTRACT WITHDRAWN |
Friday, November 8, 2013 2:36PM - 2:48PM |
D2.00004: A Physics Approach to the Repositioning of DNA Damage Sarah LeGresley, Matthew Antonik An open question in genome maintenance is how DNA repair proteins find lesions at rates that seem to exceed diffusion limited search rates. We propose a phenomenon where DNA damage induces nucleosomal rearrangements which move lesions to potential rendezvous points which are more likely to be accessible by repair proteins engaged in a random search. The feasibility of this mechanism is tested by considering the statistical mechanics of DNA containing a single lesion wrapped onto the nucleosome. We consider lesions which make the DNA either more rigid or more flexible. This can be modeled as an increase or decrease in the bending energy in a partition function of nucleosome breathing. Our results indicate that the steady state for a breathing nucleosome will most likely position the lesion at the dyad or in the linker DNA, depending on the energy of the lesion. We speculate that these positions potentially serve as rendezvous points where DNA lesions may be encountered by repair proteins which may be sterically hindered from searching the rest of the nucleosomal DNA. A more sophisticated evaluation of this proposed mechanism will require detailed information about breathing dynamics, the structure of partially wrapped nucleosomes, and the structural properties of damaged DNA. [Preview Abstract] |
Friday, November 8, 2013 2:48PM - 3:00PM |
D2.00005: Calculating free energy profiles in systems with memory effects from bi-directional pulling processes Jiong Zhang, Ioan Kosztin In biomolecules, in order to calculate kinetic quantities along a relevant reaction coordinate (RC), besides the corresponding free energy profile (potential of mean force or PMF), one also needs to properly identify the underlying stochastic model that best describes the dynamics along the RC. While there exist several methods for determining the PMF from fast non-equilibrium pulling processes, for simplicity reasons, it is generally assumed that the dynamics along the RC is that of a simple overdamped Brownian particle with known diffusion coefficient. Here we show that both the PDF and the features of the underlying non-Markov stochastic model (with memory effects), described by a generalized Langevin equation, can be determined simultaneously from properly designed bi-directional (forward and time-reversed) pulling processes. Besides the PMF, the proposed method determines the corresponding friction memory kernel, and identifies whether the diffusion along the RC is normal or anomalous (e.g., subdiffusion). The proposed method provides a novel way to analyze fast pulling data from molecular dynamics simulations and single molecule force microscopy. [Preview Abstract] |
Friday, November 8, 2013 3:00PM - 3:12PM |
D2.00006: Glass is a viable substrate for atomic force microscopy of membrane proteins Nagaraju Chada, Krishna Sigdel, Tina Matin, Raghavendar Reddy Sanganna Gari, Chunfeng Mao, Linda Randall, Gavin King Since its invention in the mid-1980s, the atomic force microscope (AFM) has become an invaluable complementary tool for studying membrane proteins in near-native environments. Historically, mica is the most common substrate utilized for biological AFM. Glass being amorphous, transparent, and optically homogeneous has its own set of advantages over mica and has the potential to broaden the use the AFM into fields that require high quality non-birefringent optical access. The use of silanized glass as AFM substrates has been reported as a means to fine tune surface chemistry. However, such coatings usually require hours of additional preparation time and can lead to increased surface roughness. In this work, we present a simple technique for preparing borosilicate glass as a substrate for two membrane systems: non-crystalline translocons (SecYEG) of the general secretary system from \textit{E. coli}, and bacteriorhodopsin (BR) from \textit{H. salinarum}. For both these membrane proteins, quantitative comparisons of the measured protein structures on glass versus mica substrates show agreement. An additional advantage of glass is that lipid coverage is rapid (\textless\ 10 minutes) and complete (occupying the entire surface). A goal is to study the bacterial export system using recently developed precision measurement techniques such as ultra-stable AFM. [Preview Abstract] |
Friday, November 8, 2013 3:12PM - 3:24PM |
D2.00007: A calibration error revealed via local tip position detection in atomic force microscopy Krishna Sigdel, Gavin King Atomic Force Microscopy (AFM) is a versatile tool in nanoscience. In conventional AFM, knowledge of the local 3D tip position is not accessible and tip trajectories are extrapolated from the cantilever deflection ($\Delta Z)$ which provides data of reduced dimensionality. The sensitivity (nm/V) of $\Delta Z$ is calibrated by taking slope of $\Delta Z $curve when the tip makes contact to a surface. Using a focused laser beam directly focused on the apex of the AFM tip, we have measured 3D positions of the tip as it interacts with a sample surface in fluid. We have observed a significant difference between the slope of ($\Delta Z)$ and that of the $Z$-tip position. This implies an erroneous calibration of sensitivity of $\Delta Z$ detection which we can now correct. Also, we have observed significant lateral slipping of tip as it touches the surface. These observations provide a comparison between tip and cantilever dynamics. [Preview Abstract] |
Friday, November 8, 2013 3:24PM - 3:36PM |
D2.00008: A novel approach to modeling photon propagation in biological tissue using the scattering signatures of spheroidal particles Vern Hart, Timothy Doyle Clinical applications of diffuse tomography require a Monte Carlo algorithm to model optical diffusion in turbid media. Of the existing algorithms, random-walk and phase function techniques are the most common. However, these approaches do not include histological information in determining subsequent photon paths. A significant amount of the optical scattering which occurs in cells has been attributed to intracellular structures, such as mitochondria, which are typically spheroidal in shape. The sphere-like cell nucleus can also become elongated during the early stages of certain cancers. The presented research introduces a novel Monte Carlo algorithm in which the scattering solution for light incident on a spheroidal particle is used to determine photon scattering directions. This technique is suggested to be a more physical description due to the inclusion of cellular properties. Diffusion profiles were generated using additional techniques for comparative purposes and significant differences were observed, indicating that the included scattering mechanism has a significant effect on the resulting diffusion. The ability to distinguish structural types in a scattered signal could potentially be used as an early diagnostic tool. [Preview Abstract] |
Follow Us |
Engage
Become an APS Member |
My APS
Renew Membership |
Information for |
About APSThe American Physical Society (APS) is a non-profit membership organization working to advance the knowledge of physics. |
© 2024 American Physical Society
| All rights reserved | Terms of Use
| Contact Us
Headquarters
1 Physics Ellipse, College Park, MD 20740-3844
(301) 209-3200
Editorial Office
100 Motor Pkwy, Suite 110, Hauppauge, NY 11788
(631) 591-4000
Office of Public Affairs
529 14th St NW, Suite 1050, Washington, D.C. 20045-2001
(202) 662-8700