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Statistical, Nonlinear, and Soft Matter Physics Commons

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Effects Of Impurities On Calcium Oxalate Crystallization As Measured By Atomic Force Microscopy, Himasha Wijesekara 2019 The University of Western Ontario

Effects Of Impurities On Calcium Oxalate Crystallization As Measured By Atomic Force Microscopy, Himasha Wijesekara

Electronic Thesis and Dissertation Repository

Calcium oxalate crystals are found in kidney stones as either calcium oxalate monohydrate (COM) or calcium oxalate dihydrate (COD). COM crystals are the most abundant form as they are thermodynamically more stable than COD crystals under physiological conditions. Certain aspartic acid-rich molecules such as osteopontin (OPN) are known to affect stone formation by inhibiting COM and COD growth. We have studied COM {010} and COD {100} faces in the presence of OPN, poly-aspartic acid (poly-ASP) and synthetic peptides derived from OPN to investigate the inhibitor mechanism.

We observed that poly-ASP preferentially inhibits one particular direction of {010} faces on COM ...


An Application Of The Ising Model, Juliano A. Everett 2019 CUNY New York City College of Technology

An Application Of The Ising Model, Juliano A. Everett

Publications and Research

Understanding how the Ising model works,what it represents, and how it can be applied to neurology. Given that an Ising model is an Entropy model that could be representative of the firing of neurons, some assumptions of the system are made and then the process is simulated through Monte Carlo methods.


From Critical Behavior To Catastrophic Runaways: Comparing Sheared Granular Materials With Bulk Metallic Glasses, Alan A. Long, Dmitry Denisov, Peter Schall, Todd C. Hufnagel, Xiaojun Gu, Wendelin J. Wright, Karin A. Dahmen 2019 University of Illinois at Urbana-Champaign

From Critical Behavior To Catastrophic Runaways: Comparing Sheared Granular Materials With Bulk Metallic Glasses, Alan A. Long, Dmitry Denisov, Peter Schall, Todd C. Hufnagel, Xiaojun Gu, Wendelin J. Wright, Karin A. Dahmen

Faculty Journal Articles

The flow of granular materials and metallic glasses is governed by strongly correlated, avalanche-like deformation. Recent comparisons focused on the scaling regimes of the small avalanches, where strong similarities were found in the two systems. Here, we investigate the regime of large avalanches by computing the temporal profile or “shape” of each one, i.e., the time derivative of the stress-time series during each avalanche. We then compare the experimental statistics and dynamics of these shapes in granular media and bulk metallic glasses. We complement the experiments with a mean-field model that predicts a critical size beyond which avalanches turn ...


Physics 516: Electromagnetic Phenomena (Fall 2019), Philip C. Nelson 2019 University of Pennsylvania

Physics 516: Electromagnetic Phenomena (Fall 2019), Philip C. Nelson

Department of Physics Papers

These course notes are made publicly available in the hope that they will be useful. All reports of errata will be gratefully received. I will also be glad to hear from anyone who reads them, whether or not you find errors: pcn@upenn.edu.


Force Oscillations Distort Avalanche Shapes, Louis W. McFaul, Wendelin J. Wright, Jordan Sickle, Karin A. Dahmen 2019 University of Illinois at Urbana-Champaign

Force Oscillations Distort Avalanche Shapes, Louis W. Mcfaul, Wendelin J. Wright, Jordan Sickle, Karin A. Dahmen

Faculty Journal Articles

Contradictory scaling behavior in experiments testing the principle of universality may be due to external oscillations. Thus, the effect of damped oscillatory external forces on slip avalanches in slowly deformed solids is simulated using a mean-field model. Akin to a resonance effect, oscillatory driving forces change the dynamics of avalanches with durations close to the oscillation period. This problem can be avoided by tuning mechanical resonance frequencies away from the range of the inverse avalanche durations. The results provide critical guidance for experimental tests for universality and a quantitative understanding of avalanche dynamics under a wide range of driving conditions.


Stability And Application Of The K-Core Dynamical Model To Biological Networks, Francesca Beatrice Arese Lucini 2019 The Graduate Center, City University of New York

Stability And Application Of The K-Core Dynamical Model To Biological Networks, Francesca Beatrice Arese Lucini

All Dissertations, Theses, and Capstone Projects

The objective of the dissertation is to illustrate the importance of the k-core dynamical model, by first presenting the stability analysis of the nonlinear k-core model and compare its solution to the most widely used linear model. Second, I show a real world application of the k-core model to describe properties of neural networks, specifically, the transition from conscious to subliminal perception.


Inference Of Language Functional Network In Healthy, Cancerous And Bilingual Brains By Fmri And Network Modeling, Qiongge Li 2019 The Graduate Center, City University of New York

Inference Of Language Functional Network In Healthy, Cancerous And Bilingual Brains By Fmri And Network Modeling, Qiongge Li

All Dissertations, Theses, and Capstone Projects

We study the underlying mechanism by which language processing occurs in the human brain using inference methods on functional magnetic resonance imaging data. The data analyzed stems from several cohorts of subjects; a monolingual group, a bilingual group, a healthy control group and one diseased case. We applied a complex statistical inference pipeline to determine the network structure of brain components involved with language. This healthy network reveals a fully connected triangular relationship between the pre-Supplementary Motor Area (pre-SMA), the Broca's Area (BA), and the ventral Pre-Motor Area (PreMA) in the left hemisphere. This "triangle'' shows consistently in all ...


Development Of A 1-Dimensional Data Assimilation To Determine Temperature And Relative Humidity Combining Raman Lidar Backscatter Measurements And A Reanalysis Model, Shayamila N. Mahagammulla Gamage 2019 The University of Western Ontario

Development Of A 1-Dimensional Data Assimilation To Determine Temperature And Relative Humidity Combining Raman Lidar Backscatter Measurements And A Reanalysis Model, Shayamila N. Mahagammulla Gamage

Electronic Thesis and Dissertation Repository

Water vapor is the most dominant greenhouse gas in Earth's atmosphere. It is highly variable and its variations strongly depend on changes in temperature. Atmospheric water vapor can be expressed as relative humidity (RH), the ratio of the partial pressure of water vapor in the mixture to the equilibrium vapor pressure of water over a flat surface of pure water at a given temperature. Liquid water can exist as super-cooled water for temperatures between 0C to -38C. Thus, RH can be measured either relative to water (RHw) or to ice (RHi). RHi measurements are important in the upper tropospheric ...


Application Of The Optimal Estimation Method (Oem) To Retrieve Relative Humidity From Raman Lidar Backscatter Measurements., Shayamila N. Mahagammulla Gamage, Robert Sica, Alexander Haefele 2019 Department of Physics and Astronomy, The University of Western Ontario, London, Canada

Application Of The Optimal Estimation Method (Oem) To Retrieve Relative Humidity From Raman Lidar Backscatter Measurements., Shayamila N. Mahagammulla Gamage, Robert Sica, Alexander Haefele

Western Research Forum

Accurate measurements of relative humidity (RH) vertical profiles in the atmosphere is important for understanding the earth's weather and the climate system. RH represent the current state of the water vapor in the atmosphere with respect to the ambient air related to saturation. Even minor changes of the RH in the lower atmosphere has a large impact of the global circulation and cloud formation. Due to its high variability RH measurements in the lower atmosphere is significantly challenging. Raman lidar is one of the potential tools that can provide vertical profiles of RH. Typically, temperature and water vapor mixing ...


Calculating The Dimensionality Of The Brain, And Other Applications Of An Optimized Generalized Ising Model In Predicting Brain's Spontaneous Functions, Pubuditha M. Abeyasinghe 2019 The University of Western Ontario

Calculating The Dimensionality Of The Brain, And Other Applications Of An Optimized Generalized Ising Model In Predicting Brain's Spontaneous Functions, Pubuditha M. Abeyasinghe

Electronic Thesis and Dissertation Repository

Understanding a system as complex as the human brain is a very demanding task. Directly working with structural and functional neuroimaging data has led to most of the understanding we have gained about the human brain. However, performing only the direct statistical comparisons on the empirical function and the structure does not fully explain the observed long-range functional correlations. Therefore, implementations of mathematical models to gain further understanding of the relationship between the structure and function of the brain is critical. Additionally, spontaneous functions of the brain can only be predicted using computer simulated models; which will be pivotal for ...


Emergent Critical Properties In Liquid-Gas Transition And Single Dislocations In Solid He4, Max Yarmolinsky 2019 Graduate Center, City University of New York

Emergent Critical Properties In Liquid-Gas Transition And Single Dislocations In Solid He4, Max Yarmolinsky

All Dissertations, Theses, and Capstone Projects

My research focuses on the analytical and numerical study of seemingly completely different systems - the classical critical point of the liquid-gas transition and a quantum topological defect (dislocation) in solid Helium-4. The unifying theme, though, is Emergence - the appearance of unexpected qualities at large distance and time scales in these systems. Our results resolve the long standing controversy about the nature of the liquid-gas criticality by showing with high confidence that it is the same as that of Ising ferromagnet. In solid 4He, a quantum superclimbing dislocation, which is expected to be violating space-time symmetry according to the elementary ...


Photo-Tunable Compression And Realization Of Colloidal Spin Ice In Skyrmion Arrays In Chiral Nematic Liquid Crystals, Yuhan Wang 2019 University of Colorado, Boulder

Photo-Tunable Compression And Realization Of Colloidal Spin Ice In Skyrmion Arrays In Chiral Nematic Liquid Crystals, Yuhan Wang

Undergraduate Honors Theses

Topological solitons are field configurations that are important to theorists in particle physics and cosmology, but recently have been studied in condensed matter systems with reconfigurable fields, like chiral magnets and liquid crystals. In these communities, there is a strong interest in studying and understanding the dynamic behavior of these solitons, many examples of which I will present in this thesis. This includes exploring the dynamic motion and patterning behavior of large number-densities of two-dimensional topological structures called skyrmions with external stimulation by light. With these techniques we can realize for the first time a colloidal spin ice system in ...


Characterization Of The Anomalous Ph Of Aqueous Nanoemulsions, Kieran P. Ramos 2019 University of Massachusetts Amherst

Characterization Of The Anomalous Ph Of Aqueous Nanoemulsions, Kieran P. Ramos

Doctoral Dissertations

Aqueous water-in-oil nanoemulsions have emerged as a versatile tool for use in microfluidics, drug delivery, single-molecule measurements, and other research. Nanoemulsions are often prepared with perfluorocarbons which are remarkably biocompatbile due to their stability, low surface tension, lipophobicity, and hydrophobicity. Therefore it is often assumed that droplet contents are unperturbed by the perfluorinated surface. However, in microemulsions, which are similar to nanoemulsions, it is known that either the pH of the aqueous phase or the ionization constants of encapsulated molecules are different from bulk solution. There is also recent evidence of low pH in perfluorinated aqueous nanoemulsions. The current underlying ...


Hydrodynamics Of Smectic Liquid Crystal Films, Eric Minor 2019 University of Colorado, Boulder

Hydrodynamics Of Smectic Liquid Crystal Films, Eric Minor

Undergraduate Honors Theses

Smectic A and C liquid crystals are capable of forming incredibly thin films, discretized by the number of molecular layers. This property makes liquid crystal films ideal for studying 2D hydrodynamics, a field of great interest both due to its fundamental importance to physics and because of its applications to biological systems. The phospholipid bilayer which makes up cell membranes is itself an ideal 2D fluid as it consists of only two layers of phospholipids, however cell membranes are incredibly small and difficult to work worth. Liquid crystal films can be several millimeters across and stable for long periods of ...


Adhesion At Solid/Liquid Interfaces, Neda Ojaghlou 2019 Virginia Commonwealth University

Adhesion At Solid/Liquid Interfaces, Neda Ojaghlou

Theses and Dissertations

The adhesion at solid/liquid interface plays a fundamental role in diverse fields and helps explain the structure and physical properties of interfaces, at the atomic scale, for example in catalysis, crystal growth, lubrication, electrochemistry, colloidal system, and in many biological reactions. Unraveling the atomic structure at the solid/liquid interface is, therefore, one of the major challenges facing the surface science today to understand the physical processes in the phenomena such as surface coating, self-cleaning, and oil recovery applications. In this thesis, a variety of theory/computational methods in statistical physics and statistical mechanics are used to improve understanding ...


The Solvation Energy Of Ions In A Stockmayer Fluid, Cameron John Shock 2019 Michigan Technological University

The Solvation Energy Of Ions In A Stockmayer Fluid, Cameron John Shock

Dissertations, Master's Theses and Master's Reports

The solvation of ions in polar solvents has been a long studied system since the early twentieth century. A common technique to calculate the energy associated with ion solvation is the Born Solvation energy equation. This equation assumes an ion is placed in an incompressible, homogeneous dielectric, which is not necessarily representative of a real system. In this work the Stockmayer Fluid Model is used in a molecular dynamics simulation through the software LAMMPS to check the quantitative correctness of the Born equation. It is also shown how solvation energies of ions placed in polymerized and non-polymerized solvents differ. It ...


Quantum Entanglement Of One-Dimensional Spinless Fermions, Emanuel Casiano-Diaz 2019 University of Vermont

Quantum Entanglement Of One-Dimensional Spinless Fermions, Emanuel Casiano-Diaz

Graduate College Dissertations and Theses

The constituents of a quantum many-body system can be inextricably linked, a phenomenon known as quantum entanglement. Entanglement can be used as a resource for quantum computing, quantum communication and detecting phase transitions, among others. The amount of entanglement can be quantified via the von Neumann and Rényi entropies, which have their origins in information theory.

In this work, the quantum entanglement between subsystems of a one dimen- sional lattice model of fermions is quantified. The von Neumann and Rényi entropies were calculated for two types of subsystems. In the first study, the subsystems were treated as two subsets of ...


Universality Class Of Explosive Percolation In Barabási-Albert Networks, Habib E. Islam, M. K. Hassan 2019 Old Dominion University

Universality Class Of Explosive Percolation In Barabási-Albert Networks, Habib E. Islam, M. K. Hassan

Physics Faculty Publications

In this work, we study explosive percolation (EP) in Barabási-Albert (BA) network, in which nodes are born with degree k = m, for both product rule (PR) and sum rule (SR) of the Achlioptas process. For m = 1 we find that the critical point tc = 1 which is the maximum possible value of the relative link density t; Hence we cannot have access to the other phase like percolation in one dimension. However, for m > 1 we find that tc decreases with increasing m and the critical exponents ν, α, β and γ for m > 1 are found to ...


Practical Chaos: Using Dynamical Systems To Encrypt Audio And Visual Data, Julia Ruiter 2019 Scripps College

Practical Chaos: Using Dynamical Systems To Encrypt Audio And Visual Data, Julia Ruiter

Scripps Senior Theses

Although dynamical systems have a multitude of classical uses in physics and applied mathematics, new research in theoretical computer science shows that dynamical systems can also be used as a highly secure method of encrypting data. Properties of Lorenz and similar systems of equations yield chaotic outputs that are good at masking the underlying data both physically and mathematically. This paper aims to show how Lorenz systems may be used to encrypt text and image data, as well as provide a framework for how physical mechanisms may be built using these properties to transmit encrypted wave signals.


Application Of Graphical Models In Protein-Protein Interactions And Dynamics, Amir Vajdi Hoojghan 2018 University of Massachusetts Boston

Application Of Graphical Models In Protein-Protein Interactions And Dynamics, Amir Vajdi Hoojghan

Graduate Doctoral Dissertations

Every organism contains a few hundred to thousands of proteins. A protein is made of a sequence of molecular building blocks named amino acids. Amino acids will be referred to as residues. Every protein performs one or more functions in the cell. In order for a protein to do its job, it requires to bind properly to other partner proteins. Many genetic diseases such as cancer are caused by mutations (changes) of specific residues which cause disturbances in the functions of those proteins.

The problem of prediction of protein binding site is a crucial topic in computational biology. A protein ...


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