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Statistical, Nonlinear, and Soft Matter Physics

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Articles 1 - 30 of 229

Full-Text Articles in Physics

Mathematical Modelling Of Temperature Effects On The Afd Neuron Of Caenorhabditis Elegans, Zachary Mobille, Rosangela Follmann, Epaminondas Rosa Nov 2020

Mathematical Modelling Of Temperature Effects On The Afd Neuron Of Caenorhabditis Elegans, Zachary Mobille, Rosangela Follmann, Epaminondas Rosa

Annual Symposium on Biomathematics and Ecology Education and Research

No abstract provided.


An Accurate Solution Of The Self-Similar Orbit-Averaged Fokker-Planck Equation For Core-Collapsing Isotropic Globular Clusters: Properties And Application, Yuta Ito Sep 2020

An Accurate Solution Of The Self-Similar Orbit-Averaged Fokker-Planck Equation For Core-Collapsing Isotropic Globular Clusters: Properties And Application, Yuta Ito

Dissertations, Theses, and Capstone Projects

Hundreds of dense star clusters exist in almost all galaxies. Each cluster is composed of approximately ten thousand through ten million stars. The stars orbit in the clusters due to the clusters' self-gravity. Standard stellar dynamics expects that the clusters behave like collisionless self-gravitating systems on short time scales (~ million years) and the stars travel in smooth continuous orbits. Such clusters temporally settle to dynamically stable states or quasi-stationary states (QSS). Two fundamental QSS models are the isothermal- and polytropic- spheres since they have similar structures to the actual core (central part) and halo (outskirt) of the clusters. The two ...


Kinetics Of The Crystal-Melt Phase Transformation In Semicrystalline Polymers, Kiran Subramaniam Iyer Jul 2020

Kinetics Of The Crystal-Melt Phase Transformation In Semicrystalline Polymers, Kiran Subramaniam Iyer

Doctoral Dissertations

The assembly of long-chain polymers into an ordered state is a process that has puzzled polymer scientists for several decades. A process that is largely controlled by the strength of intermolecular attractions in small molecular systems, this crystallization in the case of polymers is controlled by a competition between the aforementioned force of attraction between monomers and the formidable conformational entropy of polymer chains. Any factor that affects this conformational entropy, whether that is an equilibrium thermodynamic factor or a kinetic factor, has the ability to control polymer crystallization. In this thesis, we focus on understanding the underlying kinetic processes ...


Generalized Hydrodynamic Analysis Of Transport Through A Finite Open Nanopore For Two-Component Single-File Systems, King C. Lai, Tyler J. Pleasant, Andrés García, James W. Evans Jun 2020

Generalized Hydrodynamic Analysis Of Transport Through A Finite Open Nanopore For Two-Component Single-File Systems, King C. Lai, Tyler J. Pleasant, Andrés García, James W. Evans

Ames Laboratory Accepted Manuscripts

Single-file diffusion (SFD) in finite open nanopores is characterized by nonzero spatially varying tracer diffusion coefficients within a generalized hydrodynamic description. This contrasts with infinite SFD systems where tracer diffusivity vanishes. In standard tracer counterpermeation (TCP) analysis, two reservoirs, each containing a different species, are connected to opposite ends of a finite pore. We implement an extended TCP analysis to allow the two reservoirs to contain slightly different mixtures of the two species. Then, determination of diffusion fluxes through the pore allows extraction of diffusion coefficients for near-constant partial concentrations of the two species. This analysis is applied for a ...


Emergence, Mechanics, And Development: How Behavior And Geometry Underlie Cowrie Seashell Form, Michael G. Levy, Michael R. Deweese May 2020

Emergence, Mechanics, And Development: How Behavior And Geometry Underlie Cowrie Seashell Form, Michael G. Levy, Michael R. Deweese

Biology and Medicine Through Mathematics Conference

No abstract provided.


Physics 516: Electromagnetic Phenomena (Spring 2020), Philip C. Nelson May 2020

Physics 516: Electromagnetic Phenomena (Spring 2020), 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.


Target Control Of Networked Systems, Isaac S. Klickstein Apr 2020

Target Control Of Networked Systems, Isaac S. Klickstein

Mechanical Engineering ETDs

The control of complex networks is an emerging field yet it has already garnered interest from across the scientific disciplines, from robotics to sociology. It has quickly been noticed that many of the classical techniques from controls engineering, while applicable, are not as illuminating as they were for single systems of relatively small dimension. Instead, properties borrowed from graph theory provide equivalent but more practical conditions to guarantee controllability, reachability, observability, and other typical properties of interest to the controls engineer when dealing with large networked systems. This manuscript covers three topics investigated in detail by the author: (i) the ...


The Journey Of A Single Polymer Chain To A Nanopore, Navid Afrasiabian Apr 2020

The Journey Of A Single Polymer Chain To A Nanopore, Navid Afrasiabian

Electronic Thesis and Dissertation Repository

Single chain translocation has been eagerly studied for more than two decades due to its importance in biological processes and also, providing a better understanding of polymer dynamics. Polymer translocation can be divided into three stages of reaching the pore, entering the pore and passing through it. We study the delivery of the chain from the bulk to the entrance, which is called the capture process, for a single chain driven by hydrodynamic flow. Our molecular dynamics-lattice Boltzmann simulations show that the converging flow around the nanopore not only facilitates the process of finding the pore but also deforms the ...


Extended Families Of Critical And Stationary Droplets For Nonequilibrium Phase Transitions In Spatially Discrete Bistable Systems, Chi-Jen Wang, Da-Jiang Liu, James W. Evans Feb 2020

Extended Families Of Critical And Stationary Droplets For Nonequilibrium Phase Transitions In Spatially Discrete Bistable Systems, Chi-Jen Wang, Da-Jiang Liu, James W. Evans

Ames Laboratory Accepted Manuscripts

Bistable nonequilibrium systems are realized in catalytic reaction-diffusion processes, biological transport and regulation, spatial epidemics, etc. Behavior in spatially continuous formulations, described at the mean-field level by reaction-diffusion type equations (RDEs), often mimics that of classic equilibrium van der Waals type systems. When accounting for noise, similarities include a discontinuous phase transition at some value, peq, of a control parameter, p, with metastability and hysteresis around peq. For each p, there is a unique critical droplet of the more stable phase embedded in the less stable or metastable phase which is stationary (neither shrinking nor growing), and with size diverging ...


Studying Resting State And Stimulus Induced Bold Activity Using The Generalized Ising Model And Independent Component Graph Analysis, Sivayini Kandeepan Jan 2020

Studying Resting State And Stimulus Induced Bold Activity Using The Generalized Ising Model And Independent Component Graph Analysis, Sivayini Kandeepan

Electronic Thesis and Dissertation Repository

Although many technical advancements have been made, neuroscientists still struggle to explain the underlying behaviour of how brain regions communicate with each other to form large-scale functional networks. functional Magnetic Resonance Imaging (fMRI) has been commonly used to investigate changes between brain regions over time using the Blood Oxygen Level Dependent (BOLD) signal.

The goal of this thesis is to show the applicability of novel techniques and tools, such as the generalized Ising model (GIM) and the independent component graph analysis (GraphICA), to obtain information on the functional connectivity of populations with altered perception of consciousness. The GIM was used ...


Physical Models Of Living Systems 2nd Ed, New Chapter: Random Walks On An Energy Landscape, Philip C. Nelson Jan 2020

Physical Models Of Living Systems 2nd Ed, New Chapter: Random Walks On An Energy Landscape, Philip C. Nelson

Department of Physics Papers

This chapter extends the first edition of Physical Models of Living Systems (WH Freeman 2015). This preliminary version is made freely available as-is in the hope that it will be useful.


The Origins Of Phantom Partials In The Piano, Lauren M. Neldner Jan 2020

The Origins Of Phantom Partials In The Piano, Lauren M. Neldner

Honors Program Theses

Phantom partials are anomalous frequency components identifiable in the sound of the piano and occur at the sum and difference frequencies of two overtones. For several decades they have been identified as crucial components to the sound of the piano and assumed to be generated by the forced longitudinal motion of the string. Recent work has identified that contrary to common belief, most of the power is produced in the non-string components with the most likely source being the wooden structural components. This work presents experimental results for two plausible theories that could explain the origins of phantom partials in ...


Measuring And Modeling Information Flow On Social Networks, Tyson Charles Pond Jan 2020

Measuring And Modeling Information Flow On Social Networks, Tyson Charles Pond

Graduate College Dissertations and Theses

With the rise of social media, researchers have become increasingly interested in understanding how individuals inform, influence, and interact with others in their social network and how the network mediates the flow of information. Previous research on information flow has primarily used models of contagion to study the adoption of a technology, propagation of purchase recommendations, or virality of online activity. Social (or "complex") contagions spread differently than biological ("simple") contagions. A limitation when researchers validate contagion models is that they neglect much of the massive amounts of data now available through online social networks. Here we model a recently ...


Optical Potts Machine Through Networks Of Three-Photon Down-Conversion Oscillators, Mostafa Honari-Latifpour, Mohammad-Ali Miri Jan 2020

Optical Potts Machine Through Networks Of Three-Photon Down-Conversion Oscillators, Mostafa Honari-Latifpour, Mohammad-Ali Miri

Publications and Research

In recent years there has been a growing interest in optical simulation of lattice spin models for applications in classical computing. Here, we propose optical implementation of a three-state Potts spin model by using networks of coupled parametric oscillators with phase tristability. We first show that the cubic nonlinear process of spontaneous three-photon down-conversion is accompanied by a tristability in the phase of the subharmonic signal between three states with 2��/3 phase contrast. The phase of such a parametric oscillator behaves like a three-state spin system. Next, we show that a network of dissipatively coupled three-photon down-conversion oscillators emulates ...


Interpretations Of Bicoherence In Space & Lab Plasma Dynamics, Gregory Allen Riggs Jan 2020

Interpretations Of Bicoherence In Space & Lab Plasma Dynamics, Gregory Allen Riggs

Graduate Theses, Dissertations, and Problem Reports

The application of bicoherence analysis to plasma research, particularly in non-linear, coupled-wave regimes, has thus far been significantly belied by poor resolution in time, and/or outright destruction of frequency information. Though the typical power spectrum cloaks the phase-coherency between frequencies, Fourier transforms of higher-order convolutions provide an n-dimensional spectrum which is adept at elucidating n-wave phase coherence. As such, this investigation focuses on the utility of the normalized bispectrum for detection of wave-wave coupling in general, with emphasis on distinct implications within the scope of non-linear plasma physics. Interpretations of bicoherent features are given for time series ...


Dimension Reduction Techniques For High Dimensional And Ultra-High Dimensional Data, Subha Datta Dec 2019

Dimension Reduction Techniques For High Dimensional And Ultra-High Dimensional Data, Subha Datta

Dissertations

This dissertation introduces two statistical techniques to tackle high-dimensional data, which is very commonplace nowadays. It consists of two topics which are inter-related by a common link, dimension reduction.

The first topic is a recently introduced classification technique, the weighted principal support vector machine (WPSVM), which is incorporated into a spatial point process framework. The WPSVM possesses an additional parameter, a weight parameter, besides the regularization parameter. Most statistical techniques, including WPSVM, have an inherent assumption of independence, which means the data points are not connected with each other in any manner. But spatial data violates this assumption. Correlation between ...


Effects Of Impurities On Calcium Oxalate Crystallization As Measured By Atomic Force Microscopy, Himasha Wijesekara Dec 2019

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 Dec 2019

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 Nov 2019

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 ...


Characterization Of The Anomalous Ph Of Aqueous Nanoemulsions, Kieran P. Ramos Oct 2019

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 ...


Force Oscillations Distort Avalanche Shapes, Louis W. Mcfaul, Wendelin J. Wright, Jordan Sickle, Karin A. Dahmen Sep 2019

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.


Inference Of Language Functional Network In Healthy, Cancerous And Bilingual Brains By Fmri And Network Modeling, Qiongge Li Sep 2019

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

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 ...


Stability And Application Of The K-Core Dynamical Model To Biological Networks, Francesca Beatrice Arese Lucini Sep 2019

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

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.


Morphological Study Of Voids In Ultra-Large Models Of Amorphous Silicon, Durga Prasad Paudel Aug 2019

Morphological Study Of Voids In Ultra-Large Models Of Amorphous Silicon, Durga Prasad Paudel

Dissertations

The microstructure of voids in pure and hydrogen-rich amorphous silicon (a:Si) network was studied in ultra-large models of amorphous silicon, using classical and quantum- mechanical simulations, on the nanometer length scale. The nanostructure, particularly voids of device grade ultra-large models of a:Si was studied, in which observed three-dimensional realistic voids were extended using geometrical approach within the experimental limit of void-volume fractions. In device-grade simulated models, the effect of void morphology; size, shape, number density, and distribution on simulated scattering intensities in small- angle region were investigated. The evolution of voids on annealing below the crystallization temperature (≤ 800 ...


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 Jul 2019

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 ...


Reactive And Stimuli-Responsive Sulfonium-Based Polymer Zwitterions, Cristiam Santa Chalarca Jul 2019

Reactive And Stimuli-Responsive Sulfonium-Based Polymer Zwitterions, Cristiam Santa Chalarca

Doctoral Dissertations

This dissertation describes the synthesis and characterization of novel monomers and (co)polymer zwitterions that incorporate trialkylsulfonium cations. The novel materials presented herein constitute a unique type of polymer zwitterions that exhibit salt- and temperature-dependent water solubility as well as inherent reactivity. The behavior of these polymers in aqueous solutions, as nanostructures, and at liquid-liquid interfaces was studied; in all cases, the inherent reactivity of the polymers was harnessed towards the fabrication of novel polymers and soft materials.

Following an introductory chapter, Chapter 2 describes the synthesis of sulfonium sulfonate monomers and polymer zwitterions. Both styrenic and methacrylic monomers were ...


Application Of The Optimal Estimation Method (Oem) To Retrieve Relative Humidity From Raman Lidar Backscatter Measurements., Shayamila N. Mahagammulla Gamage, Robert Sica, Alexander Haefele Jun 2019

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 Apr 2019

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 ...


Characterization Of The Motion Of Cellulose Synthase Protein Complexes In The Plant Cell Membrane, Nina Zehfroosh Mar 2019

Characterization Of The Motion Of Cellulose Synthase Protein Complexes In The Plant Cell Membrane, Nina Zehfroosh

Doctoral Dissertations

The polysaccharide cellulose is the main component of plant cell walls, so it is the most abundant polymer on Earth. While it is widely used in industry due to its remarkable properties, such as renewability and biodegradability, its biosynthesis is still not well understood. The large transmembrane protein Cellulose Synthase Complex (CSC) is responsible for synthesizing cellulose by polymerizing UDP glucose into the constituent glucan chains of cellulose.

In this project, I used variable angle epi-fluorescence microscopy (VAEM) in combination with single-particle tracking to characterize the motion of GFP labeled CSCs in the hypocotyl of Arabidopsis thaliana (A. thaliana) seedlings ...


Emergent Critical Properties In Liquid-Gas Transition And Single Dislocations In Solid He4, Max Yarmolinsky Feb 2019

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

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 ...