Bulletin of the American Physical Society
14th Annual Meeting of the Northwest Section of the APS
Volume 57, Number 7
Thursday–Saturday, October 18–20, 2012; Vancouver, British Columbia, Canada
Session H2: Biological and Applied Physics |
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Chair: Michael Schick, University of Washington Room: SFU Harbour Centre 1315 Scotiabank Lecture Room |
Saturday, October 20, 2012 1:30PM - 2:06PM |
H2.00001: Biological membranes at large length scales: Biological applications and computational modeling Invited Speaker: Lutz Maibaum Biological membranes, such as the plasma membrane surrounding cells, perform an astonishing variety of essential functions: they provide structural support, regulate trafficking, and control endocytosis and fusion events, among others. Some of these capabilities are due to a membrane's elastic properties: at typical length scales of hundreds of nanometers, it can be thought of as a two-dimensional fluid sheet that exhibits significant fluctuations. This mesoscopic picture can be used to model several biological processes, including the formation of cellular protrusions due to interactions between the cytoskeleton and the cell membrane. We show that a membrane can bundle polymerizing actin filaments, thereby enabling the formation of tubular structures that resemble filopodia observed in motile cells. To study this and similar processes that involve the cell membrane over large length scales, we have developed a new computational model that correctly captures the effects of bending rigidity and fluidity. We show that our model exhibits an elastic response to perturbations that is consistent with the Canham-Helfrich description of lipid bilayers, while also providing a computationally efficient way to capture the effects of shape fluctuations. [Preview Abstract] |
Saturday, October 20, 2012 2:06PM - 2:42PM |
H2.00002: Membranes, mechanics, and intracellular transport Invited Speaker: Raghuveer Parthasarathy Cellular membranes are remarkable materials -- self-assembled, flexible, two-dimensional fluids. Understanding how proteins manipulate membrane curvature is crucial to understanding the transport of cargo in cells, yet the mechanical activities of trafficking proteins remain poorly understood. Using an optical-trap based assay involving dynamic deformation of biomimetic membranes, we have examined the behavior of Sar1, a key component of the COPII family of transport proteins. We find that Sar1 from yeast (\textit{S. cerevisiae}) lowers membrane rigidity by up to 100{\%} as a function of its concentration, thereby lowering the energetic cost of membrane deformation. Human Sar1 proteins can also lower the mechanical rigidity of the membranes to which they bind. However, unlike the yeast proteins, the rigidity is not a monotonically decreasing function of concentration but rather shows increased rigidity and decreased mobility at high concentrations that implies interactions between proteins. In addition to describing this study of membrane mechanics, I'll also discuss some topics relevant to a range of biophysical investigations, such as the insights provided by imaging methods and open questions in the dynamics of multicellular systems. [Preview Abstract] |
Saturday, October 20, 2012 2:42PM - 2:54PM |
H2.00003: Effect of Sterol Structure on Chain Ordering of an Unsaturated Phospholipid: A 2H-NMR Study of POPC/Sterol Membranes Mehran Shaghaghi, Jenifer Thewalt, Martin Zuckermann The physical properties of biological membranes are considerably altered by the presence of sterols. In particular, sterols help to maintain the integrity of the cell by adjusting the fluidity of the plasma membrane. Cholesterol is in addition an important component of lipid rafts which are hypothesized to compartmentalize the cell membrane surface thereby making it possible for certain proteins to function. Using 2H-NMR spectroscopy, we studied the effect of a series of different sterols on the chain ordering of POPC, an unsaturated phospholipid present in eukaryotic cell membranes. We were able to assigned specific roles to the structural differences between the sterols by comparing the manner in which they affect the average lipid chain conformation of POPC. [Preview Abstract] |
Saturday, October 20, 2012 2:54PM - 3:06PM |
H2.00004: Frequency Mapping of Rat Spinal Cord at 7T Evan Chen, Alexander Rauscher, Piotr Kozlowski, Andrew Yung The spinal cord is an integral part of the nervous system responsible for sensory, motor, and reflex control crucial to all bodily function. Due to its non-invasive nature, MRI is well matched for characterizing and imaging of spinal cord, and is used extensively for clinical applications. Recent developments in magnetic resonance imaging (MRI) at high field (7T) using phase represents a new approach of characterizing spinal cord myelin. Theory suggests that microstructure differences in myelinated white matter (WM) and non-myelinated gray matter (GM) affect MR phase, measurable frequency shifts. Data from pilot experiments using a multi-gradient echo (MGE) sequence to image rat spinal cords placed parallel to main magnetic field B0 has shown frequency shifts between not only between WM and GM, but also between specific WM tracts of the dorsal column, including the fasciculus gracilis, fasciculus cuneatus, and corticospinal tract. Using MGE, frequency maps at multiple echo times (TE) between 4ms and 22ms show a non-linear relationship between WM frequency, contrary to what was previously expected. These results demonstrate the effectiveness of MGE in revealing new information about spinal cord tissue microstructure, and lays important groundwork for in-vivo and human studies. [Preview Abstract] |
Saturday, October 20, 2012 3:06PM - 3:18PM |
H2.00005: Combined Fat Imaging/Look Locker for mapping of lipid spin-lattice (T1) relaxation time Annie Jihyun Park, Andrew Yung, Piotr Kozlowski, Stefan Reinsberg Tumor hypoxia is a main problem arising in the treatment of cancer due to its resistance to cytotoxic therapy such as radiation and chemotherapy, and selection for more aggressive tumor phenotypes. Attempts to improve and quantify tumor oxygenation are in development and tools to assess the success of such schemes are required. Monitoring oxygen level with MRI using T1 based method (where oxygen acts as T1 shortening agent) is a dynamic and noninvasive way to study tumor characteristics. The method's sensitivity to oxygen is higher in lipids than in water due to higher oxygen solubility in lipid. Our study aims to develop a time-efficient method to spatially map T1 of fat inside the tumor. We are combining two techniques: Fat/Water imaging and Look Locker (a rapid T1 measurement technique). Fat/Water Imaging is done with either Dixon or Direct Phase Encoding (DPE) method. The combination of these techniques poses new challenges that are tackled using spin dynamics simulations as well as experiments in vitro and in vivo. [Preview Abstract] |
Saturday, October 20, 2012 3:18PM - 3:38PM |
H2.00006: BREAK |
Saturday, October 20, 2012 3:38PM - 3:50PM |
H2.00007: How Tongue Size and Roughness Affect Lapping M.J. Hubbard, K.M. Hay The biomechanics of domestic cat lapping (Felis catus) and domestic dog lapping (Canis familiaris) is currently under debate. Lapping mechanics in vertebrates with incomplete cheeks, such as cats and dogs, is a balance of inertia and the force of gravity likely optimized for ingestion and physical necessities. Physiology dictates vertebrate mass, which dictates vertebrate tongue size, which dictates lapping mechanics to achieve optimum liquid ingestion; with either touch lapping, scooping, or a hybrid lapping method. The physics of this optimized system then determines how high a column of liquid can be raised before it collapses due to gravity, and therefore, lapping frequency. Through tongue roughness model variation experiments it was found that pore-scale geometrical roughness does not appear to affect lapping or liquid uptake. Through tongue size model variation experiments it was found that there is a critical tongue radius in the range of 25 mm to 35 mm above which touch lapping is no longer an efficient way to uptake liquid. Vertebrates with incomplete cheeks may use a touch lapping method to ingest water if their tongue radius is less than this critical radius and use an alternative ingestion method if their tongue radius is larger. [Preview Abstract] |
Saturday, October 20, 2012 3:50PM - 4:02PM |
H2.00008: Rayleigh-Taylor Instability in Disintegration of Liquid Globule due to Constant Acceleration Maziyar Jalaal, Kian Mehravaran Fragmentation of droplets is of fundamental importance in several applications, from volcanic eruption to combustion engines. In the current study, the fragmentation of an initially spherical droplet accelerated by a constant body force is examined in 3D. A finite volume-volume of fluid (FV-VOF) numerical technique is employed for direct numerical simulation (DNS) of the two-phase system. The numerical code uses a combination of octree spatial discretization and a multilevel Poisson solver. It is shown that the fragmentation has four main steps: 1-Deformation of the initially spherical droplet and bag formation. 2-Bursting of the bag generating upper and lower tori. 3-Deformation and breakup of the tori. 4-Disintegration of remaining ligaments and drops. The role of Rayleigh-Taylor instability (RTI) at each step is studied in detail. It is showed RTI is the prevailing mechanism in bursting of the bag, flattened core and tori. Stability analyses are also provided based on the linearized Navier-Stokes equations, and the most amplified wave numbers were compared with the observations in DNS. Reasonable agreement is observed between the numerical and analytical solutions. [Preview Abstract] |
Saturday, October 20, 2012 4:02PM - 4:14PM |
H2.00009: Particle dynamics in a virtual harmonic potential Momcilo Gavrilov, Yonggun Jun, John Bechhoefer The recently developed Anti-Brownian ELectrokinetic (ABEL) trap is a device for trapping and manipulating single fluorescent particles in solution. The ABEL trap acquires an image of a Brownian particle in order to estimate its position and then apply an electrical force to bring it to the desired position. This feedback system allows us to explore properties of a single molecule in its natural environment. Although the ABEL trap has been used in a number of biophysical studies, there is no complete theory to describe how the ABEL trap actually works. In this talk, we will present the first complete theory of the ABEL trap that takes into account parameters such as the particle's diffusion constant, feedback frequency, camera exposure time, observational noise, response delay, and feedback gain. The theory predicts successfully the power spectrum density of particle motion for given trap parameters. We will present the case of an imposed harmonic virtual potential, comparing theoretical predictions to simulation and experimental results. [Preview Abstract] |
Saturday, October 20, 2012 4:14PM - 4:26PM |
H2.00010: Studying biomechanics at the single-molecule level with optical tweezers Naghmeh Rezaei, Nancy Forde, Andrew Wieczorek Lasers have found significant roles in today's world. One of their applications is trapping microscopic objects, which has helped scientists to understand mechanical processes involved in protein and DNA mechanics, structure, and interaction kinetics. We use the optical trapping technique to study mechanical properties of short proteins that play a vital role in providing structural support for the body. Elastin and collagen are two important structural proteins: we study their mechanical response to an applied force, and try to understand how it relates to their biological roles. The goals are to reveal how changes chemical compositions at the molecular scale affect mechanical properties, and relate these to macroscopic changes that can lead to serious and sometimes lethal diseases. [Preview Abstract] |
Saturday, October 20, 2012 4:26PM - 4:38PM |
H2.00011: A Density Functional Theory of Transfer Free Energy in Protiens Eric Mills, Steven Plotkin The cell environment in which proteins fold and function is crowded with biological molecules, at densities of $\sim$300g/L. Treating these molecules explicitly in a MD simulation introduces enormous computational cost, so accurate ways of modelling their contribution to protein behaviour is desirable. I will discuss existing models of transfer free energy (Auton and Bolen, Biochemistry 43, 1329) and solvation (Luchko et al, J Chem Thry Cmp it 6, 607) and propose a new approach, which uses classical density functional theory (Emborsky et al, Fluid Phase Equil 306, 15) to calculate the effect of these solutes on protein folding in a way that is efficient, yet accurate. The theory developed will be applied to both post-processing approaches and implicit solvent models. [Preview Abstract] |
Saturday, October 20, 2012 4:38PM - 4:50PM |
H2.00012: Solvation effects on like-charge attraction Shahzad Ghanbarian Alavijeh, Joerg Rottler We present results of molecular dynamics simulations on electrostatic interaction between two parallel charged rods in the presence of divalent counterions. Such polyelectrolytes have been considered as a simple model for understanding electrostatic interaction in biomolecules such as DNA. Since there are correlations between the free charge carriers, the phenomenon of like charge attraction appears for specific parameters. We explore the effects of the nonlocal dielectric function of water on this peculiar phenomenon. The behavior of the force between the charged rods in a simulation model with full representation of water molecules are completely different from a model in which water is modeled as a continuum dielectric with $\epsilon_r=72$. After calculating counterion-rodion pair correlation functions, we find that the presence of water molecules changes the distribution of counterions in the system and explains the difference in the behavior of the force in two models. [Preview Abstract] |
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