Biological and Chemical Physics Commons^™

Fibration Symmetries Uncover The Building Blocks Of Biological Networks, Flaviano Morone, Ian Leifer, Hernán A. Makse

Publications and Research

A major ambition of systems science is to uncover the building blocks of any biological network to decipher how cellular function emerges from their interactions. Here, we introduce a graph representation of the information flow in these networks as a set of input trees, one for each node, which contains all pathways along which information can be transmitted in the network. In this representation, we find remarkable symmetries in the input trees that deconstruct the network into functional building blocks called fibers. Nodes in a fiber have isomorphic input trees and thus process equivalent dynamics and synchronize their activity. Each …

Magnetic Resonance Studies Of Free Radicals Generation And Their Impact In Different Polymers, Sunita Humagain

Dissertations, Theses, and Capstone Projects

Studies of free radicals in the physics, chemistry, biology, and materials science have contributed to advancements in those fields. The presence of radicals can damage the material and system in some instances and, in some cases, they may enhance the property of the material as well. Knowledge of free radical transformations helps in resilience of certain polymers and inhibition of the oxidation of food and medicine. In this thesis, using the magnetic resonance techniques, EPR and NMR, the generation of free radicals and their effect on the structure of the material is being studied.

Kapton Polyimide (PI, Kapton®) used in …

Supercharged Models Of Intrinsically Disordered Proteins And Their Utility In Sensing, Peter J. Schnatz

Dissertations, Theses, and Capstone Projects

In this thesis I show that greatly increasing the magnitude of a protein’s net charge using surface supercharging transforms that protein into a ligand-gated or counterion-gated conformational molecular switch. To demonstrate this I first modified the designed helical bundle hemoprotein H4 using simple molecular modeling, creating a highly charged protein which both unfolds reversibly at low ionic strength and undergoes the ligand-induced folding transition commonly observed in signal transduction by intrinsically disordered proteins in biology. Due to the high surface charge density, ligand binding to this protein is allosterically activated by low concentrations of divalent cations and the polyamine spermine. …

Pregnancy Induced Alterations Of Reproductive Tract Collagen And Elastin In A Murine Model, Basant K. Dhital

Dissertations, Theses, and Capstone Projects

This thesis reports on structural and dynamical modifications of reproductive tract elastin and collagen as a function of parity. Pelvic floor dysfunction, including pelvic organ prolapse (POP) is a major concern affecting female health worldwide, leading to surgeries costing billions of dollars annually. Collagen, elastic fibers, and proteoglycans are major extracellular matrix (ECM) components found in connective tissues. Vaginal child birth, advancing age, and disruption or dysfunction of connective tissue are major risk factors of POP. In the female reproductive tract, the assembly of elastic fibers is crucial for the pelvic floor support. Any disturbance in the synthesis, assembly, and …

Information Content, Charge Transport Properties, And Computational Capacities Of Proteins, Joseph Murphy Brisendine Jr.

Dissertations, Theses, and Capstone Projects

This thesis is the beginning of an attempt to build a coherent theory of the properties of proteins based in information theory and the duality of information theory and nonequilibrium thermodynamics. Throughout, we will adopt the viewpoint that information can act as a thermodynamic potential, which is necessary to understand how biological processes are both enabled and constrained by the laws of thermodynamics. Understanding information as a form of thermodynamic potential also clarifies the description of proteins and other biological macromolecules as “molecular machines”: meso-scale structures with emergent causal powers which perform work on their environments by irreversibly dissipating energy …

Stochastic Resonance In A Proton Pumping Complex I Of Mitochondria Membranes, Davneet Kaur, Ilan Filonenko, Lev Mourokh, Cornelius Fendler, Robert H. Blick

Publications and Research

We make use of the physical mechanism of proton pumping in the so-called Complex I within mitochondria membranes. Our model is based on sequential charge transfer assisted by conformational changes which facilitate the indirect electron-proton coupling. The equations of motion for the proton operators are derived and solved numerically in combination with the phenomenological Langevin equation describing the periodic conformational changes. We show that with an appropriate set of parameters, protons can be transferred against an applied voltage. In addition, we demonstrate that only the joint action of the periodic energy modulation and thermal noise leads to efficient uphill proton …

Continuum Electrostatics Analysis Of The Kok Cycle Of Photosystem Ii, Witold Szejgis

Dissertations, Theses, and Capstone Projects

The Kok cycle is catalytic process by which the oxygen-evolving complex (OEC) of photosystem II (PSII) oxidizes two water molecules forming oxygen. Four OEC oxidation states (S₀ to S₃) in the Kok cycle precede the final product formation in the S₄ state. Here a semi-empirical classical electrostatics analysis is applied to S₀ to S₃ states of the OEC is used to estimate the electrochemical midpoints for each S-state transition and the proton loss coupled to oxidation. To account for geometrical rearrangement within the cluster during Kok cycle optimized QM/MM geometries are used for each …

Second Harmonic Generation – A Novel Approach In Retinal Imaging, Denis Y. Sharoukhov

Dissertations, Theses, and Capstone Projects

Here we present the utilization of Second Harmonic Generation (SHG) for label-free imaging of microtubules (MTs) in the retinal nerve fiber layer (RNFL). MTs are an important part of axonal cytoskeleton, providing structural support and serving as a railroad in intracellular transport. We demonstrate the application of SHG microscopy to the following studies: 1) Can changes in MT conformation be detected when treated with a stabilizing drug (Taxol); 2) if disruption in MT precedes loss of axons in a mouse model of glaucoma (DBA/2J); and 3) if elevated levels of intraocular pressure affect MT integrity. Our results validate SHG imaging …

Rules And Mechanisms For Efficient Two-Stage Learning In Neural Circuits, Tiberiu Teşileanu, Bence Ölveczky, Vijay Balasubramanian

Publications and Research

Trial-and-error learning requires evaluating variable actions and reinforcing successful variants. In songbirds, vocal exploration is induced by LMAN, the output of a basal ganglia-related circuit that also contributes a corrective bias to the vocal output. This bias is gradually consolidated in RA, a motor cortex analogue downstream of LMAN. We develop a new model of such two-stage learning. Using stochastic gradient descent, we derive how the activity in ‘tutor’ circuits (e.g., LMAN) should match plasticity mechanisms in ‘student’ circuits (e.g., RA) to achieve efficient learning. We further describe a reinforcement learning framework through which the tutor can build its teaching …

Classical Transport In Disordered Systems, Antonios Papaioannou

Dissertations, Theses, and Capstone Projects

This thesis reports on the manifestation of structural disorder on molecular transport and it consists of two parts. Part I discusses the relations between classical transport and the underlying structural complexity of the system. Both types of molecular diffusion, namely Gaussian and non-Gaussian are presented and the relevant time regimes are discussed. In addition the concept of structural universality is introduced and connected with the diffusion metrics. One of the most robust techniques for measuring molecular mean square displacements is magnetic resonance. This method requires encoding and subsequently reading out after an experimentally controlled time, a phase ϕ to the …

A Principle Of Economy Predicts The Functional Architecture Of Grid Cells, Xue-Xin Wei, Jason Prentice, Vijay Balasubramanian

Publications and Research

Grid cells in the brain respond when an animal occupies a periodic lattice of ‘grid fields’ during navigation. Grids are organized in modules with different periodicity. We propose that the grid system implements a hierarchical code for space that economizes the number of neurons required to encode location with a given resolution across a range equal to the largest period. This theory predicts that (i) grid fields should lie on a triangular lattice, (ii) grid scales should follow a geometric progression, (iii) the ratio between adjacent grid scales should be √e for idealized neurons, and lie between 1.4 and 1.7 …

Wave Function For Harmonically Confined Electrons In Time-Dependent Electric And Magnetostatic Fields, Hong-Ming Zhu, Jin-Wang Chen, Xiao-Yin Pan, Viraht Sahni

Publications and Research

We derive via the interaction “representation” the many-body wave function for harmonically confined electrons in the presence of a magnetostatic field and perturbed by a spatially homogeneous time-dependent electric field—the Generalized Kohn Theorem (GKT) wave function. In the absence of the harmonic confinement – the uniform electron gas – the GKT wave function reduces to the Kohn Theorem wave function. Without the magnetostatic field, the GKTwave function is the Harmonic Potential Theorem wave function. We further prove the validity of the connection between the GKT wave function derived and the system in an accelerated frame of reference. Finally, we provide …

Wave Function For Time-Dependent Harmonically Confined Electrons In A Time-Dependent Electric Field, Yu-Qi Li, Xiao-Yin Pan, Viraht Sahni

Publications and Research

The many-body wave function of a system of interacting particles confined by a time-dependent harmonic potential and perturbed by a time-dependent spatially homogeneous electric field is derived via the Feynman path-integral method. The wave function is comprised of a phase factor times the solution to the unperturbed time-dependent Schrödinger equation with the latter being translated by a time-dependent value that satisfies the classical driven equation of motion. The wave function reduces to that of the Harmonic Potential Theorem wave function for the case of the time-independent harmonic confining potential.