Physics
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Item STABILITY AND SCALING OF NEURONAL AVALANCHES AND THEIR RELATIONSHIP TO NEURONAL OSCILLATIONS(2019) Miller, Stephanie Regina; Roy, Rajarshi; Biophysics (BIPH); Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)The generation of cortical dynamics in awake mammals is not yet fully understood. However, it is known that neurons leverage distinct organizational schemes to achieve behavior and cognitive function, and that this precise spatiotemporal organization may go awry in illness. In 2003, a form of scale-free synchrony termed “neuronal avalanches” was first observed by Beggs & Plenz in cultured cortical tissue and later confirmed in rodents, nonhuman primates, and humans. In this dissertation, we draw from monkey and rodent studies to demonstrate that neuronal avalanches capture key features of neural population activity and constitute a robust and stable (e.g. self-organized) indicator of balanced excitation and inhibition in cortical networks. We also show for the first time that neuronal avalanches and oscillations co-exist in frontal cortex of nonhuman primates and identify the avalanche temporal shape as a biomarker predicated upon critical systems theory. Finally, we present progress towards characterizing altered avalanche dynamics in a developmental mouse model for schizophrenia using 2-photon calcium imaging in awake animals.Item THEORETICAL AND COMPUTATIONAL STUDIES OF HUMAN INTERPHASE CHROMOSOMES(2019) Shi, Guang; Thirumalai, Devarajan; Biophysics (BIPH); Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)In this thesis, various aspects of dynamical and structural properties of human interphase chromosomes are studied using both theoretical and computational tools. In addition, the cooperative transport by the multi-motor system was investigated using a stochastic kinetic model. First, I create the Chromosome Copolymer Model (CCM) by representing chromosomes as a copolymer. I first showed that the model is consistent with current experimental data. Using the CCM, I further investigated the dynamics of human interphase chromosomes. The model suggested that human interphase chromosome exhibit glassy-like dynamics characterized by sluggish movement, large loci-to-loci variations, and dynamical heterogeneity. Furthermore, I predicted that human interphase chromosomes also display extensive structural heterogeneity. Using a theoretical framework I developed based on polymer physics, I am able to identify that the existence of subpopulations is the reason for the Hi-C-FISH paradox. As an application of the theory, the information of subpopulations of cells can be readily extracted from experimental FISH data. The results suggest that heterogeneity is pervasive in genome organization at all length scales, reflecting large cell-to-cell variations. Then I proceed to develop a method to reconstruct the three-dimensional genome structure directly from Hi-C data. By applying the theory combined with various manifold embedding methods to experimental Hi-C data, I am able to visualize the averaged global 3D organization of a single chromosome and also local structures such as Topological Associated Domains. The method provides a fast and simple way to help experimentalist visualize the genome organization from the measured Hi-C data. Finally, I propose a kinetic model for the multi-motor system. I investigate the effect of mechanical coupling between multiple motors on their velocity and force-velocity behavior. Reduction of velocity is observed for coupled motor system especially when the coupling strength is strong. The model also shows that the multi-motors system is more efficient for transporting large cargo but is less efficient for transporting small cargo compared to a single motor.Item LIPID FORCE FIELD PARAMETERIZATION FOR IMPROVED MODELING OF ION-LIPID INTERACTIONS AND ETHER LIPIDS, AND EVALUATION OF THE EFFECTS OF LONG-RANGE LENNARD-JONES INTERACTIONS ON ALKANES(2019) Leonard, Alison N; Klauda, Jeffery B; Biophysics (BIPH); Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Chemical specificity of lipid models used in molecular dynamics simulations is essential to accurately represent the complexity and diversity of biological membranes. This dissertation discusses contributions to the CHARMM36 (C36) family of lipid force fields, including a revised model for the glycerol-ether linkage found in plasmalogens and archaeal membranes; interaction parameters between ions and lipid oxygens; and evaluation of the effects of long-range Lennard-Jones parameters on alkanes. Long-range Lennard-Jones interactions have a significant impact on structural and thermodynamic properties of systems with nonpolar regions such as membranes. Effects of these interactions on properties of alkanes are investigated. Implementation of the Lennard-Jones particle-mesh Ewald (LJ-PME) method with the C36 additive and Drude polarizable force fields improves agreement with experiment for thermodynamic and kinetic properties of alkanes, with Drude outperforming the additive FF for nearly all quantities. Trends in the temperature dependence of the density and isothermal compressibility are also improved. Phospholipids containing an ether linkage between the glycerol backbone and hydrophobic tails are prevalent in human red blood cells and nerve tissue. Ab initio results are used to revise linear ether parameters and develop new parameters for the glycerol-ether linkage in lipids. The new force field, called C36e, more accurately represents the dihedral potential energy landscape and improves solution properties of linear ethers. C36e allows more water to penetrate an ether-linked lipid bilayer, increasing the surface area per lipid compared to simulations carried out with the original C36 parameters and improving structural properties. In addition to modulating membrane structure, lipid-ion interactions influence protein-ligand binding and conformations of membrane-bound proteins. Interaction parameters are introduced describing Be2+ affinity for binding sites on lipids. Experimental binding affinities reveal that Be2+ strongly binds to phosphoryl groups. Revised interaction parameters reproduce binding affinities in solution simulations. In a separate effort, experimental results for the radius of gyration (R_g) of polyethylene glycol (PEG) in various concentrations of KCl reveal that, while C36e parameters reproduce experimental R_g of PEG in the absence of KCl, adding salt results in underestimation of〖 R〗_g. It is found that the water shell around PEG affects R_g calculated from neutron scattering experiments, and K+-PEG interactions increase the gauche character of PEG.Item IMPROVING THE SPEED AND OPTICAL SECTIONING OF FLUORESCENCE MICROSCOPY TECHNIQUES FOR BIOPHYSICAL ANALYSIS OF SUBCELLULAR PROCESSES(2019) Giannini, John; Losert, Wolfgang; Biophysics (BIPH); Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)This dissertation focuses on novel fluorescence microscopy techniques and the biophysical analysis of cell biology enabled by such techniques. Modern cell biology research benefits greatly from the ability to accurately visualize the inner workings of cells. Fluorescence microscopy is particularly well suited to imaging live cells, as it is gentle enough to avoid damaging cells, provides sufficient spatial resolution to image small cellular features, and targets and visualizes specific cell structures and processes with high contrast. An additional feature that is often desirable in fluorescence microscopy is the ability to image rapidly enough to freeze the motion of dynamic cell processes, yet technical limitations make imaging with both high spatial and temporal resolution challenging. In this thesis I address methods for improving the speed, spatial resolution, and optical sectioning of fluorescence microscopy techniques. I then apply some of these innovations to study actin structures and dynamics in epithelial cells. Because of its role in driving cellular motion, targeted studies of the actin cytoskeleton using fluorescence microscopy can be used to examine cell migration dynamics. In both in vivo and in vitro experiments, I use high spatiotemporal resolution fluorescence microscopy techniques to provide insight into the role of the actin cytoskeleton in responding to external structural stimuli.Item A BIOPHYSICAL PERSPECTIVE ON COLLECTIVE CELL MIGRATION AND MATHEMATICAL MODELING IN PHYSICS FOR THE LIFE SCIENCES(2018) Hemingway, Deborah; Losert, Wolfgang; Redish, Edward F; Biophysics (BIPH); Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)This dissertation pulls from the fields of physics, biology, and education to address novel problems both in current biological research on collective cell migration and in a reformed introductory physics for life science (IPLS) course. In collective cell migration, cells communicate with each other via a number of means including via signaling pathways. In developing zebrafish, a select group of cells called the posterior lateral line primordium (pLLp) is known to communicate with each other via two types of signaling pathways, Wnt and Fgf. In this work, we examine another signaling pathway, BMP, to gain insight into its role in the migratory behavior of the pLLp. My results demonstrate that BMP signaling is vital to successful migration and show that BMP affects the cohesiveness (cell-cell adhesions), directionality (direction of migration), and migratory speed of the cells in the pLLp. These results and insight were obtained through both modeling the biological system and utilizing concepts and analytical tools prevalent in physics. As part of the continuing reforms for the IPLS courses at the University of Maryland, College Park (UMD) I proposed and developed a novel methodology for curriculum development that is based on my own experimental biophysics research on collective cell migration. As a researcher, I used the tools and principles of physics to gain insight in the biological system and in parallel, I propose that “cross-disciplinary authenticity” is achieved when the tools and principles of one discipline are utilized to gain insight into a secondary discipline. I outline the methodology for achieving such, include an example problem set that is based on my research, and discuss the results from the deployment of the problem set in the IPLS course.Item Effect of electrostatic interactions on biomolecular self-assembly processes(2018) Xu, Hongcheng; Matysiak, Silvina; Biophysics (BIPH); Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Molecular level self-assembly processes are not only ubiquitous in living cells, but also widely applied in industry to synthesize and fabricate a variety of nanoscale biomaterials. The emergence of ordered aggregates from disordered components typically requires driving forces from electrostatic interactions to hydrophobic-hydrophilic effects. This thesis aims to elucidate the effect of electrostatic interactions, and the intricate balance between electrostatic and hydrophobic interactions in dictating spontaneous self-assembly processes with three case studies covering various types of biomolecules. For the first case study, we have examined the pH-induced polysaccharide hydrogel network formation. The polysaccharide molecule chitosan forms hydrogels composed of water-filled cross-linking polymer chains. The pH-responsive selfassembly behavior of chitosan hydrogel has been utilized in fabricating nanomaterials with a wide range of applications. To investigate the role of electrostatic interactions in the chitosan hydrogel network formation, we have developed a novel coarse-grained (CG) chitosan polymer model that captures the pH-dependent self-assembly behavior. The structural, mechanical, and thermodynamical properties of chitosan polymer hydrogel have been characterized well in the simulations and agree very well with experimental observations. For the second case study, the anticancer peptide folding induced by phospholipid membrane was investigated. Peptide folding in an aqueous environment is a self-assembly process that has been well studied over the years. However, the folding in a membranous environment is complicated by the heterogeneity in phospholipid distributions and membrane-peptide interactions. To provide information about the driving forces behind membrane peptide folding and the effect of lipid composition on folding behavior, my work has combined our recently developed Water-Explicit Polarizable Protein (WEPPRO) and Membrane (WEPMEM) model to explore the driving forces behind model anticancer peptide SVS-1 folding and how they can be affected by changing the membrane composition. For the third case study, we have studied the formation of nanodomains in mixed lipid bilayers. Phospholipid membranes are essential components in animal cells. The heterogeneous distribution of phospholipids on the membrane bilayer plays an important role in cellular structure and function such as signal transduction and membrane fusion. Interactions between a mixture of lipids and different ligands give rise to interesting patterns that are yet to be understood. Model lipid bilayers with a content of anionic lipids have been shown experimentally to be sensitive to the presence of certain ions. Monovalent cation Li+ induces membrane phase transition similarly as Ca2+ and Mg2+, while distinctive from other monovalent cations like Na+ and K+. We have evaluated the role of electrostatics interactions in the sizedependent cation-induced lipid nanodomain formation with binary mixed bilayers composed of zwitterionic and anionic lipids.Item UNDERSTANDING CELL DIFFERENTIATION AND MIGRATION WITH MULTIVARIATE CELL SHAPE QUANTIFICATION(2018) Chen, Desu; Losert, Wolfgang; Biophysics (BIPH); Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)This thesis focuses on developing multivariate quantification methods of cell shape to facilitate understanding of physiological processes such as cell differentiation and migration. Cell shape reflects complex intracellular and extracellular factors affecting cell function. However, analyses associating cell shape and cell function need to account for challenges of multivariate interpretation, single-cell heterogeneity and reproducibility. Specifically, Human Bone Marrow Stromal Cells (hBMSCs) population in nanofiber scaffolds can develop osteogenic differentiation without chemical cues. I developed a method based on Support Vector Machine (SVM) to train classifiers as boundaries in the shape metric spaces to identify the day 1 cell shape phenotype of hBMSCs population in nanofiber scaffolds. To reduce the effect of single-cell heterogeneity in the population phenotyping, the “supercell” method was introduced to generate average measurements of small groups of cells for SVM training. To overcome the multivariate complexity in biological interpretation, a feature selection process was implemented to select the most significant cell shape metrics. The predictive potential of the achieved classifiers was validated by subsampling. It was found that in nanofiber scaffolds, hBMSCs were narrower with more elongated and dendritic shape and rougher cell boundary. Further, I found that increase in nanofiber density enhanced hBMSCs osteogenic differentiation potential. The pre-trained classifiers successfully predict the modulation of nanofiber density on hBMSCs fates and single-cell shape. While much can be learned from cell shapes alone, it is important to note that shapes can change with time, especially for migrating cells. The second part of my thesis focuses on analysis of shape dynamics. Quantification for cell shape dynamics at the subcellular level was developed to understand the coordination of the subcellular myosin localization and the cell boundary dynamics in neutrophil migration in vivo. The correlation of myosin localization and positive cell boundary curvature was identified as a unique in vivo neutrophil migration phenotype. Correlations of myosin localization and local cell boundary dynamics in vivo were found to be affected by cell motility and polarization. This analysis framework shown here can also be used to study the link between other subcellular features and neutrophil migration and shape dynamics.Item UNCOVERING THE BIOPHYSICAL MECHANISMS OF HISTONE COMPLEX ASSEMBLY(2018) Zhao, Haiqing; Papoian, Garegin A.; Biophysics (BIPH); Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)At the most basic level, inheritance in living beings occurs by passing the genomic information such as the DNA sequences from the parent generation to the offspring generation. Hence, it is a fundamental goal for every generation to efficiently express the genomic information and safely pass it on to the next generation. In human and other eukaryotic species, this mission is mediated via chromatin, a macromolecule with intricate hierarchical structure. The fundamental unit of chromatin is called a nucleosome, a complex of histone proteins wrapped around with DNA. To carry out diverse biological functions such as transcription and DNA replication, the DNA-protein complex must dynamically transition between more compact, closed states and more accessible, open ones. To fully understand the chromatin structure and dynamics, it is essential to comprehend the basic structural unit of chromatin, nucleosome. In this dissertation, I present my doctoral research in the exploration of the nucleosome dynamics problem, focusing on the assembly process of histone proteins. From histone monomer to dimer, then to tetramer, octamer, and nucleosome, I used different computational modeling theories and techniques, together with different experimental collaborations, to investigate the overall thermodynamics and specific mechanistic details of nucleosome dynamics at different levels. My work has shed light on the fundamental principles governing the histone protein folding and histone complex assembly, in particular, highlighting similarities and differences between the canonical and variant CENP-A histones.Item NANOSCALE THERMODYNAMICS OF MECHANOSENSITIVE ION CHANNELS AND THEIR ROLE IN THE MECHANISM OF OSMOTIC FITNESS OF MICROBES(2018) Cetiner, Ugur; Sukharev, Sergei; Biophysics (BIPH); Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Bacterial mechanosensitive channels are major players in cells’ ability to cope with hypo-osmotic stress. Excess turgor pressure due to fast water influx is reduced as the channels, triggered by membrane tension, open and release osmolytes. In bacteria, the bulk release of ions and other osmolytes is mainly mediated by two families of mechanosensitive channels: MscS and MscL. The MscL family channels form large non-selective pathways in the membrane and gate near the lytic tension. In this way, they act as a final back up mechanism against osmotic downshock. MscS family channels require less tension to open and display great diversity in structure and functionality. Chapter 2 describes the first multifaceted phenomenological study of the emergency osmolyte release system in wild type Pseudomonas aeruginosa in comparison with E.coli. We recorded the kinetics of cell equilibration reported by light scattering responses to osmotic up- and down-shocks using the stopped-flow technique. We also performed the first electrophysiological characterization of the mechanosensitive ion channels in Pseudomonas aeruginosa. We presented a quantitative biophysical description of “osmotic fitness” which would be of interest to microbiologists, epidemiologists, ecologists and general environmental scientists. Chapter 3 presents the combined theoretical and experimental analysis of the full functional cycle of the bacterial channel MscS, which plays a major role in osmotic adjustments and environmental stability of most bacteria. We modeled MscS gating as a finite state continuous-time Markov chain and obtained analytical expressions for the steady state solution and the inactivated state area (which is experimentally hard to determine). In Chapter 4, we derived a general formalism to extract the free energy difference between the closed and open states of mechanosensitive ion channels (ΔF) from non-equilibrium work distributions associated with the channels’ gating. Our new approach bridges the gap between recent developments in non-equilibrium thermodynamics of small systems and ion channel biophysics. Our study also serves as an experimental verification of non-equilibrium work relations in a biological system. Therefore, the results in this thesis are sufficiently general and would be of interest to a broad community.Item UNCOVERING FUNDAMENTAL MECHANISMS OF ACTOMYOSIN CONTRACTILITY USING ANALYTICAL THEORY AND COMPUTER SIMULATION(2018) Komianos, James Eric; Papoian, Garegin A; Biophysics (BIPH); Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Actomyosin contractility is a ubiquitous force-generating function of almost all eukaryotic organisms. While more understanding of its dynamic non-equilibrium be- havior has been uncovered in recent years, little is known regarding its self-emergent structures and phase transitions that are observed in vivo. With this in mind, this thesis aims to develop a state-of-the-art computational model for the simulation of actomyosin assemblies, containing detailed cytosolic reaction-diffusion processes such as actin filament treadmilling, cross-linker (un)binding, and molecular motor walking. This is explicitly coupled with novel mechanical potentials for semi-flexible actin filaments. Then, using this simulation framework combined with other ana- lytical approaches, we propose a novel mechanism of contractility in a fundamental actomyosin structural element, derived from a thermodynamic free energy gradi- ent favoring overlapped actin filament states when passive cross-linkers are present. With this spontaneous cross-linking, transient motors such as non-muscle myosin II can generate robust network contractility in a collective myosin II-cross-linker ratcheting mechanism. Finally, we map the phases of contractile behavior of disor- dered actomyosin using this theory, showing explicitly the cross-linking, motor and boundary conditions required for geometric collapse or tension generation in a net- work comprised of those elements. In this theory, we move away from the sarcomeric contractility mechanism typically reconciled in disordered non-muscle structures. It is our hope that this study adds theoretical knowledge as well as computational tools to study the diverse contractile assemblies found in non-muscle actomyosin networks.