Fall 2014 Schedule


Date Speaker
28 August Anthony Hazel (Gumbart Lab)
4 September Bradford Taylor (Weitz Lab)
11 September Guillermo Amador (Hu Lab)
18 September Vlad Levenfeld (Goldman Lab)
25 September Bye Week
2 October Paul Cardenas Lizana (Zhu Lab)
9 October Jairo Rodriguez Padilla (Fenton Lab)
16 October Will Ratcliff – School of Biology, Georgia Tech
23 October Dan Kovari (Curtis Lab)
30 October Perrin Schiebel (Dan Goldman)
6 November Yanyan ‘Claire’ Ji (Fenton Lab)
13 November Alexis Noel (Hu Lab)
20 November Kahye Song – Pohang University of Science & Technology, Pohang, KOR
27 November Thanksgiving Break
4 December Sulisay Phonekeo (Hu Lab)

Fall 2014 Abstracts

20 November 2014

Kahye Song — School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology (POSTECH),

What enables the plants to move?

Most plants have been considered as non-motile organisms. However, plants move in response to environmental changes for survival. In addition, some species drive dynamic motions in a short period of time. Mimosa pudica is a plant that rapidly shrinks its body in response to external stimuli. It has specialized organs that are omnidirectionally activated due to morphological features. In addition, scales of pinecone open or close up depending on humidity for efficient seed release. A number of previous studies on the dynamic motion of plants have been investigated in a biochemical point of view. However, an interdisciplinary study on the structural characteristics of the motile plant should be accompanied by biophysical research to explain the principles underlying such movements. In this study, the motions of plants were analyzed and morphological characteristics of those motile organs were investigated by using X-ray CT and micro-imaging techniques. The results show that the dynamic motions of motile plants are supported by structural features related with water transport. These studies would provide new insight for better understanding the moving mechanism of motile plant in morphological point of view.

13 October 2014

Alexis Noel — Hu Lab

To catch a fly: The role of saliva adhesivity during prey capture in frog tongue projection.

There are many organisms that utilize a sticky biological fluid to capture prey, such as amphibians, pitcher plants, sundew plants and spider silk. At a molecular scale, these bio-adhesives are composed of long chain glycoprotein networks, which give the fluids unique adhesive properties through viscoelasticity. Strain hardening is observed in these fluids during normal separation; extensional viscosity increases by orders of magnitude as strain rate increases. In the field, there is not currently a method to test and compare biological adhesives. While professional extensional rheometers, such as the CaBER or FiSER, provide accurate measurements, they are expensive and not portable. Many biological samples (such as saliva) degrade within hours; once the sample reaches the machine, the fluid properties may have changed dramatically. We have designed and built a portable extensional rheometer (titled Elo-Rheo) which allows us to analyze biological fluid properties in the field, minimizing degradation of the fluid sample. The machine is lightweight, user-friendly and costs less than $1500. By analyzing these bio-adhesives, we can determine forces apparent in the fluid during prey capture. In this experimental study, we investigate how a frog’s sticky saliva enables high-speed prey capture. At the Atlanta zoo, we use high-speed video to film the trajectory of frog tongues during projection; post analysis of the video allows us to calculate acceleration during insect impact and retraction. Using a frog saliva sample in Elo-Rheo, we can mimic separation rates present during prey capture and so infer the adhesive force between tongue and prey. High speed collection using soft, adhesive materials has numerous applications. Current actuated systems in the field of soft robotics operate at low speeds, and are mostly used for machine movement. This work will inspire new methods to quickly collect an object with non-uniform surface texture in such a way that minimizes destructive collision forces.

6 November 2014

Yanyan ‘Claire’ Ji — Fenton Lab

Modeling on Calcium Dynamics and Contraction

At present, there are close to a hundred mathematical models describing the electrophysiology and dynamics of single cardiomyocytes. However, most of them focus only on ion channels and sarcoplasmic reticulum (SR) dynamics without including the equations to simulate their contraction. This is a considerable drawback since electrical activities and mechanics are closely related. In this study, we present a systematical methodology to incorporate a contraction model (Negroni_Lascano_1996) into fourteen well known electrophysiological (EP) cell models. To evaluate how well these coupled electromechanical (EM) models behave, we study them using a postextrasystolic pacing (PESP) protocol. We first compare the dynamics between the new EM models and the original EP models to quantify the effects of the inclusion of contraction on the EP models. Then we compare the contractile strength of the new EM models with previously published experiments (Yue et al 1985). Finally we compare results from the Negroni_Lascano_1996 model with two other contraction models. We discover that the original EP models with dynamic troponin buffers show little change in dynamics after the implementation of contraction, and these models also better match the experimental contractile strength data than models originally with instantaneous or no troponin buffers. We conclude and describe how EP models with dynamic buffers are better candidates to incorporate contraction.

30 October 2014

Perrin Schiebel — Goldman Lab

Limbless locomotion in heterogeneous terrestrial substrates

Snakes can traverse heterogeneous terrain composed of rocks, foliage, soil and/or sand. Previous research elucidated how rigid obstacles influence snake locomotion by studying a model heterogeneous terrain—symmetric lattices of obstacles placed in hard ground. We want to understand the benefits and tradeoffs of different substrate-body interaction modes during transit of substrates composed of rigid obstacles and flowable (granular) substrates in desert-adapted snakes. We hypothesize that, due to these snakes’ ability to utilize granular resistive forces, introducing a granular medium (GM) to a peg lattice will improve performance (in terms of snake speed) compared to that in the same lattice on a hard substrate. We tested Chionactis occipitalis, the Mojave shovel-nosed snake, in a square lattice of 0.64 cm diameter obstacles arrayed on both a hard, slick substrate and in a GM of 270±4 μm diameter glass particles (comparable in size to natural sand). We challenged the snakes to move through lattices of different densities such that nearest-neighbor spacing ranged from slightly wider than the body diameter to larger than the snakes’ natural amplitude. Performance was a function of both lattice spacing and substrate. Kinematics were similar for both substrates but depended on lattice density: at low density, undulatory locomotion was typically used while at high density a more complicated time-dependent body shape emerged.

23 October 2014

Daniel Kovari — Curtis Lab

Modeling Phagocytosis: Using Hydrodynamics to Predict Cell Behavior

Phagocytosis is the process by which individual cells engulf foreign bodies. It is the hallmark behavior of white blood cells, being the process through which those cells ingest and degrade pathogens and debris. Comprehensive models of phagocytosis hold the promise of providing key insights into processes such as infection, wound repair and drug delivery. The cascade of biochemical signals which trigger phagocytosis is expansive. Furthermore, it is often unclear how to integrate the results of purified molecular experiments into a larger whole-cell model. Consequently, modeling phagocytosis from the ground up is not only computationally expensive but also ill-posed. As an alternative, our work seeks to model phagocytosis as a mechanical process. I present physical characterizations of phagocytosis and our efforts to develop a simple hydrodynamic model built around physical properties which can be measured on intact living cells. The model predicts phagocyte behavior in a planar geometry, termed frustrated phagocytosis, and can be extended to make predictions for other cell-substrate interactions.

16 October 2014

Will Ratcliff — School of Biology, Georgia Inst. of Technology

Experimental Evolution of Multicellularity

The evolution of multicellularity was one of the most significant innovations in the history of life, but early steps in this transition remain poorly understood. Using experimental evolution, we demonstrate that keys steps in this transition evolve far more easily than previously thought. Starting with the unicellular yeast Saccharomyces cerevisiae, we evolved clustering genotypes characterized by production of multicellular propagules, a juvenile phase, and determinate growth. We observe a shift in the level of selection, such that clusters evolve as multicellular individuals, resulting in the evolution of simple among-cell division of labor. Over thousands of generations of adaptation, we see the emergence of morphological complexity in our multicellular yeast (though they are still quite simple).

9 October 2014

Jairo Rodriguez — Fenton Lab

Interaction of Scroll Rings in Reaction Diffusion Equations

2 October 2014

Paul Cardenas Lizana — Zhu Lab

Mechanically-regulated pathways employed by viruses to escape immune recognition: An atomistic study

One subset of leukocytes is cytotoxic T lymphocytes (CD8+ T cells) that are capable of inducing cytolytic activity on cells presenting foreign antigen peptide. T cell receptors (TCR) expressed on CD8+ T cells interacts with peptide and class I Major Histocompatibility Complex (MHC) molecule on antigen presenting cells. TCR found on each T cell is unique in that they are specific in scanning pMHC complexes. Antigens are foreign substances that induce immune response. Antigens are composed of several antigenic determinants, known as epitopes, and the epitopes can bind to a specific TCR and/or antibody.

Viral persistence is observed in Cytomegalovirus (CMV) and Hepatitis C (HCV) infection. CMV does not pose a threat to an immune competent subject in terms of developing a life-threatening disease; however infected subject with HCV evolves to chronic state during the course of infection. The development into chronic condition is linked in part to the rise of “viral mutations” that have decreased functional effects as those of the wild type (WT) thereby escaping recognition from the immune system. Nevertheless, the true extent of TCR-pMHC interaction, its role in the molecular mechanism of antigen recognition, and the tolerance of leukocytes to viral epitopes upon infection, still remain a speculative issue, largely due to the lack of experimental approaches that could definitively address this question. TCR/pMHC interaction must also stand mechanical forces in order to prevent dissociation from external fluid flow or substrate stresses.

MD simulation combined with experiments are employed to understand the mechanically-regulated pathways of TCR-pMHC interaction in the context of viral infection and epitope recognition. It will be described the molecular mechanisms by which mutant epitopes escape detection by the immune system and correlate this loss of recognition by the TCR with a characteristic mechanical behavior of TCR-pMHC response (catch-slip/slip-only bond) This kind of study is novel and provides a unique means for elucidating the mechanical regulation of bio-molecular interactions at the atomic resolution.

18 September 2014

Vlad Levenfeld — Goldman Lab

The role of ground-reaction forces in martial arts striking techniques

The human body is capable of generating powerful impact forces through elaborate combinations of movements, which is particularly evident in combat sports such as boxing and mixed martial arts. In order to understand the complex dynamics of such movements, studies have been done on the kinematics and impact forces of various punches. In other sports, notably running and gymnastics, the features of ground reaction forces in time are used to understand the biomechanical strategies used by the athlete. However, there is little in the way of such analysis for combat sports. Most combat sports studies involving dynamometry focus on the impact force of the punch. The overall contribution of the legs to the force of the punch has been examined, but little research has been done on the features of the GRF trajectory in time. We hypothesize that there are signatures in these time-domain signals that can qualitatively and quantitatively differentiate the strikes of experienced fighters versus less experienced fighters. To observe the GRF during an athlete’s strike, we constructed a platform with a force plate at the center and synchronized the recorded signals with two high-speed cameras. We predict that careful analysis of the GRF signature and synchronized video will yield a deeper understanding of the biomechanical strategies used during punching, as it has for other sports.

11 September 2014

Guillermo Amador — Hu Lab

Arrayed bristles reduce soiling of compound eyes

While the presence of bristle arrays on insect compound eyes has been known for quite some time, there hasn’t been a study analyzing the effect of bristles on airborne particle deposition. Our hypothesis is that bristles affect incoming airflows to reduce airborne particle deposition to the eye surface. Through collaboration with Dr. Isao Shimoyama’s lab at the University of Tokyo, micron-scaled sensors are used to probe the effect of bristle arrays on incoming airflows. The sensors are comprised of piezo-resistive cantilevers that deflect when acted upon by the dynamic pressure exerted by flowing air. When deflected, the electrical resistance of the cantilever is changed. The change in resistance of the cantilever is proportional to the dynamic pressure exerted by the airflow, so it can be used as a metric for the intensity of the airflow. Through the use of these sensors, we find that bristle arrays greatly affect airflow penetration for shearing flows, reducing the dynamic pressure by 40-60%. The decrease in flow penetration observed in this study may motivate bio-inspired solutions for reducing airborne particle deposition onto sensitive surfaces.

4 September 2014

Bradford Taylor — Weitz Lab

A Hitchhiker’s Guide to Coinfection: Ecology and Evolution of Virophage

Virophage are viruses of viruses that serve a hyperparasitic role. In order to reproduce, the virophage must coinfect a eukaryotic host along with a giant virus. There are two ways for the virophage to hitchhike into coinfection: by adhering to the virus and the pair later entering the host, or by entering the host and lying in wait for the virus. I will address the different effects between these modes of coinfection on the population dynamics of the system. I will also look at the feasibility of multiple virophage strains coexisting and the existence of virophage capable of both modes of coinfection.

28 August 2014

Anthony Hazel — Gumbart Lab

Molecular Dynamics Simulations of Small Protein Structures

Molecular dynamics (MD) simulations provide atomistic detail to biological and chemical processes. It is used extensively in the study of protein structure and folding. Here, I use the power of MD simulations to determine the folding pathway and energetics of small protein structures, namely α-helices and β-turns. Extensive computational work has been performed on small Ala-based peptides due to Ala’s high helical propensity amongst the 20 common amino acids. The free energy of α-helix formation of deca-alanine in vacuum is often used as a benchmark for free energy calculation methods. A common reaction coordinate used to describe the folding pathway and the stability of the helical and extended states is the end-to-end distance of the peptide, which shows a helical minimum around 14-15 Å which is ~20-25 kcal/mol more stable than the fully extended state. We first calculated this folding free energy in water to get a better description of α-helix formation in vivo. We discovered that near the α-helical minimum, end-to-end distance becomes highly degenerate. Therefore, we introduced a second reaction coordinate – α-helical content – and calculated a 2D free energy surface, which revealed the extended states to be of comparable free energy to the helical state due to hydrogen bonding from the surrounding water molecules, a result not seen in previous free energies calculated for deca-alanine in water using only end-to-end distance. Lastly, I will show how these results can be extended to other folding systems, e.g. α-helix formation inside the protein exit tunnel of the ribosome during translation, β-turn formation of the GB1 protein, and β-helix formation of the virulence factors for autotransporters in the outer membrane of gram-negative bacteria.