Open Access. Powered by Scholars. Published by Universities.®

Digital Commons Network

Open Access. Powered by Scholars. Published by Universities.®

PDF

2006

University of Pennsylvania

Discipline
Keyword
Publication
Publication Type

Articles 1 - 30 of 861

Full-Text Articles in Entire DC Network

Effect Of Supercoiling On Formation Of Protein-Mediated Dna Loops, Prashant K. Purohit, Philip C. Nelson Dec 2006

Effect Of Supercoiling On Formation Of Protein-Mediated Dna Loops, Prashant K. Purohit, Philip C. Nelson

Departmental Papers (MEAM)

DNA loop formation is one of several mechanisms used by organisms to regulate genes. The free energy of forming a loop is an important factor in determining whether the associated gene is switched on or off. In this paper we use an elastic rod model of DNA to determine the free energy of forming short 50–100 basepair, protein mediated DNA loops. Superhelical stress in the DNA of living cells is a critical factor determining the energetics of loop formation, and we explicitly account for it in our calculations. The repressor protein itself is regarded as a rigid coupler; its ...


A Review Of Three Techniques For Formally Representing Variable Binding, Jeffrey A. Vaughan Dec 2006

A Review Of Three Techniques For Formally Representing Variable Binding, Jeffrey A. Vaughan

Technical Reports (CIS)

This paper compares three models for formal reasoning about programming languages with binding. Higher order abstract syntax (HOAS) uses meta-level binding to represent object-level binding [PE88]. Nominal Logic couples a concrete representation of bound variables with a formal apparatus for safely manipulating bound variables [Pit03]. The locally named binding representation places bound and free variables in different syntactic sorts [MP99]. This paper surveys each binding model, and compares it to the others and to Gordon and Melham’s axiomatization of the untyped lambda calculus [GM97]. Comparisons are made based on expressive power, transparency to human readers, and suitability for mechanized ...


Finite State Abstraction Of A Stochastic Model Of The Lactose Regulation System Of Escherichia Coli, Agung Julius, Ádám Halász, R. Vijay Kumar, George J. Pappas Dec 2006

Finite State Abstraction Of A Stochastic Model Of The Lactose Regulation System Of Escherichia Coli, Agung Julius, Ádám Halász, R. Vijay Kumar, George J. Pappas

Departmental Papers (MEAM)

This paper focuses on the lactose regulation system in Escherichia coli bacteria, one of the most extensively studied examples of positive feedback in a naturally occurring gene network. State-of-the-art nonlinear dynamical system models predict a bi-stability phenomenon that is confirmed in experiments. However, such deterministic models fail to explain experimental observations of spontaneous transition between the two stable states in the system and the simultaneous occurrence of both steady states in a population of cells. In this paper, we propose a stochastic model that explains this phenomenon. Furthermore, we also extract a coarser two-state continuous-time Markov chain as a higher ...


Density Functions For Navigation Function Based Systems, Savvas G. Loizou, Ali Jadbabaie Dec 2006

Density Functions For Navigation Function Based Systems, Savvas G. Loizou, Ali Jadbabaie

Lab Papers (GRASP)

In this paper, we present a scheme for constructing density functions for systems that are almost globally asymptotically stable (i.e., systems for which all trajectories converge to an equilibrium except for a set of measure zero) based on navigation functions. Although recently-proven converse theorems guarantee the existence of density functions for such systems, results are only existential and the construction of a density function for almost globally asymptotically stable systems remains a challenging task. We show that for a specific class of dynamical systems that are defined based on a navigation function, a density function can be easily derived ...


How Should Global Society Address Climate Change? - The Kyoto Protocol And Its Future, Takeshi Hamada Dec 2006

How Should Global Society Address Climate Change? - The Kyoto Protocol And Its Future, Takeshi Hamada

Master of Environmental Studies Capstone Projects

This research paper explores how global society should address climate change, focusing on the Kyoto Protocol and its future.
In the introduction, the paper presents three challenges that we face in addressing climate change; uncertainty, trade-off between environment and economy, and political conflict. The paper tries to work out how to address climate change with these three challenges in mind.


Guiding Youth To Careers: Do Mentoring Programs Benefit Urban Youth?, Matthew R. Malone Dec 2006

Guiding Youth To Careers: Do Mentoring Programs Benefit Urban Youth?, Matthew R. Malone

CUREJ - College Undergraduate Research Electronic Journal

Mentoring programs have become a popular method for helping to close the achievement gap in education. Few research studies have been conducted to support the benefits of these programs, and questions have been raised about school-based mentoring which is short in duration and less intensive than traditional mentoring. This research focuses on the Guiding Youth to Careers program run through the Center for Community Partnerships at the University of Pennsylvania. The research shows that if specific goals are outlined and completed, school-based mentoring programs can have an impact on the students they serve.


Comment On "Optical Response Of Strongly Coupled Metal Nanoparticles In Dimer Arrays", Vadim A. Markel Dec 2006

Comment On "Optical Response Of Strongly Coupled Metal Nanoparticles In Dimer Arrays", Vadim A. Markel

Departmental Papers (BE)

I have recalculated the extinction spectra of aggregates of two silver nanospheres shown in Figs. 2 and 3 of the paper by J. J. Xiao, J. P. Huang, and K. W. Yu [Phys. Rev. B 71, 045404 (2005)]. I have used the approximate method of images according to the formulas published in that reference and an exact numerical technique. I have found that the three sets of data those I have obtained by the method of images, the numerical results, and the results published in the reference in question do not coincide. In this Comment, I discuss the reasons for ...


A Multiscale Computational Approach To Dissect Early Events In The Erb Family Receptor Mediated Activation, Differential Signaling, And Relevance To Oncogenic Transformations, Yingting Liu, Jeremy Purvis, Andrew Shih, Joshua Weinstein, Neeraj Agrawal, Ravi Radhakrishnan Dec 2006

A Multiscale Computational Approach To Dissect Early Events In The Erb Family Receptor Mediated Activation, Differential Signaling, And Relevance To Oncogenic Transformations, Yingting Liu, Jeremy Purvis, Andrew Shih, Joshua Weinstein, Neeraj Agrawal, Ravi Radhakrishnan

Departmental Papers (BE)

We describe a hierarchical multiscale computational approach based on molecular dynamics simulations, free energy-based molecular docking simulations, deterministic network-based kinetic modeling, and hybrid discrete/continuum stochastic dynamics protocols to study the dimermediated receptor activation characteristics of the Erb family receptors, specifically the epidermal growth factor receptor (EGFR). Through these modeling approaches, we are able to extend the prior modeling of EGF-mediated signal transduction by considering specific EGFR tyrosine kinase (EGFRTK) docking interactions mediated by differential binding and phosphorylation of different C-terminal peptide tyrosines on the RTK tail. By modeling signal flows through branching pathways of the EGFRTK resolved on a ...


Chlorine Adsorption Induced Structure And Energetics Change Of Vinyl Chloride Physisorbed On Ag(1 1 1), David B. Pursell, John M. Vohs, Hai-Lung Dai Dec 2006

Chlorine Adsorption Induced Structure And Energetics Change Of Vinyl Chloride Physisorbed On Ag(1 1 1), David B. Pursell, John M. Vohs, Hai-Lung Dai

Departmental Papers (CBE)

On the Ag(1 1 1) surface pre-adsorbed with Cl, TDS and HREELS studies find that vinyl chloride physisorbs molecularly with a binding energy 8 kJ/mol stronger and an adsorption geometry more parallel to the surface in comparison with adsorption on clean Ag(1 1 1). The vinyl chloride in close proximity to the surface Cl has stronger binding energy than the ones further removed from Cl. The binding energy change due to surface Cl can be modeled with charge-dipole interaction between the negatively charged Cl and the large molecular dipole of vinyl chloride.


Evaluating The Use Of Fairmount Dam Fish Passage Facility By Anadromous Fishes In The Schuylkill River, Philadelphia, Pennsylvania, Joseph A. Perillo Jr. Dec 2006

Evaluating The Use Of Fairmount Dam Fish Passage Facility By Anadromous Fishes In The Schuylkill River, Philadelphia, Pennsylvania, Joseph A. Perillo Jr.

Master of Environmental Studies Capstone Projects

The Schuylkill River in Southeaster Pennsylvania once supported massive spring runs of anadromous fishes until the construction of dams in the early 1800's. American shad (Alosa sapidissima), striped bass (Morone saxatilis), and river herring (alewife Alosa pseudoharengus and blueback herring A. aestivalis) ascended the Schuylkill River as far upstream as Pottsville (160 rkm), but have not done so since 1820, when Fairmount Dam (13.6 rkm) was built. The dam served as a physical barrier to migratory fishes, completely blocking upstream movement and access to critical spawning grounds. In 1979, a vertical slot fish passage facility was constructed on ...


Structure And Hydrogen Bonding In Casid1+ X: Issues About Covalent Bonding, Hui Wu, Wei Zhou, Terrence J. Udovic, John J. Rush, Taner Yildirim Dec 2006

Structure And Hydrogen Bonding In Casid1+ X: Issues About Covalent Bonding, Hui Wu, Wei Zhou, Terrence J. Udovic, John J. Rush, Taner Yildirim

Departmental Papers (MSE)

We report here our high-resolution neutron powder diffraction and neutron vibrational spectroscopy study of CaSiD1+x along with first-principles calculations, which reveal the deuterium structural arrangements and bonding in this novel alloy hydride. Both the structural and spectroscopic results show that, for x > 0, D atoms start occupying a Ca3Si interstitial site. The corresponding Si-D bond length is determined to be 1.82 Å, fully 0.24 Å larger than predicted by theory. Thus, our neutron measurements are at odds with the strongly covalent Si-H bonding in CaSiH1+x that such calculations suggest, a result which ...


Review Of Mark D. Bennett And Joan Mciver Gibson, A Field Guide To Good Decisions: Values In Action, Vardit Ravitsky Dec 2006

Review Of Mark D. Bennett And Joan Mciver Gibson, A Field Guide To Good Decisions: Values In Action, Vardit Ravitsky

Center for Bioethics Papers

Decisions are something we all face. Decisions change our lives. As parents, as community members, as professionals, we find ourselves daily in complex situations that require good decision-making. Most decisions impact not only the decision maker, but also a network of others whose lives they affect. For healthcare providers and clinical bioethicists, decisions lie at the heart of daily practice and are particularly challenging as they touch the lives of individuals who are often vulnerable and in need of guidance and clarity.


Unity In Identity, Disunity In Execution: Expressions Of French National Identity At The 1937 Paris World’S Fair, Peter Feldman Dec 2006

Unity In Identity, Disunity In Execution: Expressions Of French National Identity At The 1937 Paris World’S Fair, Peter Feldman

CUREJ - College Undergraduate Research Electronic Journal

The 1937 Paris World’s Fair was a celebration of “peace” and “progress” at time when the continent was about to descend into total war. In this era of feuding ideologies and hyper-competitive nationalism, France’s attempt to project an idealized national identity fell scattered. A closer examination of three examples of French architecture—the Palais de Chaillot, the Regional Pavilions, and the Pavilion de Temps Nouveaux—illustrate that this idealized portrayal of unity was undermined by the execution of the buildings themselves. The result was a much more accurate picture of the country during the inter-war period.


New Maps Of The Library: Building Better Subject Discovery Tools Using Library Of Congress Subject Headings, John Mark Ockerbloom Dec 2006

New Maps Of The Library: Building Better Subject Discovery Tools Using Library Of Congress Subject Headings, John Mark Ockerbloom

Scholarship at Penn Libraries

We describe tools in development at the University of Pennsylvania to generate and display interactive "subject maps" for exploring library collections. Based on the Library of Congress Subject Headings (LCSH), these maps are automatically built from existing authority records, a collection's bibliographic records, and optional local "tweaks" for local interests and search patterns. Users can explore these maps via ordinary text- based web browsing, and browse clusters of related research resources. We now provide these maps for small collections like The Online Books Page, and are experimenting with maps for the entire Penn Library catalog. We hope to enable ...


Near-Field Scanning Optical Tomography: A Nondestructive Method For Three-Dimensional Nanoscale Imaging, Jin Sun, P. Scott Carney, John C. Schotland Dec 2006

Near-Field Scanning Optical Tomography: A Nondestructive Method For Three-Dimensional Nanoscale Imaging, Jin Sun, P. Scott Carney, John C. Schotland

Departmental Papers (BE)

We present the theoretical foundation for near-field scanning optical tomography, a method for three-dimensional optical imaging with subwavelength resolution. An analysis of the forward problem for both scalar and vector optical fields is described. This is followed by the construction of the pseudoinverse solution to the linearized inverse scattering problem. The results are illustrated by numerical simulations.


Sampling-Based Algorithm For Testing And Validating Robot Controllers, Jongwoo Kim, Joel M. Esposito, R. Vijay Kumar Dec 2006

Sampling-Based Algorithm For Testing And Validating Robot Controllers, Jongwoo Kim, Joel M. Esposito, R. Vijay Kumar

Departmental Papers (MEAM)

The problem of testing complex reactive control systems and validating the effectiveness of multi-agent controllers is addressed. Testing and validation involve searching for conditions that lead to system failure by exploring all adversarial inputs and disturbances for errant trajectories. This problem of testing is related to motion planning. In both cases, there is a goal or specification set consisting of a set of points in state space that is of interest, either for finding a plan, demonstrating failure or for validation. Unlike motion planning problems, the problem of testing generally involves systems that are not controllable with respect to disturbances ...


Weak Input-To-State Stability Properties For Navigation Function Based Controllers, Savvas G. Loizou, R. Vijay Kumar Dec 2006

Weak Input-To-State Stability Properties For Navigation Function Based Controllers, Savvas G. Loizou, R. Vijay Kumar

Departmental Papers (MEAM)

Due to topological constraints, Navigation Functions, are not, except from trivial cases, equivalent to quadratic Lyapunov functions, hence systems based on Navigation Functions cannot directly accept an Input-to-State stability (ISS) characterization. However a relaxed version of Input-to-State stability, namely almost global ISS (aISS), is shown to be applicable. The proposed framework provides compositional capability for navigation function based systems. Cascade as well as feedback interconnections of aISS navigation systems are shown to also possess the aISS property under certain assumptions on the interconnections. Several simulated examples of navigation systems are presented to demonstrate the effectiveness of the proposed scheme.


Voice Over Sensor Networks, Rahul Mangharam, Anthony Rowe, Raj Rajkumar, Ryohei Suzuki Dec 2006

Voice Over Sensor Networks, Rahul Mangharam, Anthony Rowe, Raj Rajkumar, Ryohei Suzuki

Real-Time and Embedded Systems Lab (mLAB)

Wireless sensor networks have traditionally focused on low duty-cycle applications where sensor data are reported periodically in the order of seconds or even longer. This is due to typically slow changes in physical variables, the need to keep node costs low and the goal of extending battery lifetime. However, there is a growing need to support real-time streaming of audio and/or low-rate video even in wireless sensor networks for use in emergency situations and shortterm intruder detection. In this paper, we describe a real-time voice stream-capability in wireless sensor networks and summarize our deployment experiences of voice streaming across ...


Suicide Gene Delivery By Calcium Phosphate Nanoparticles: A Novel Method Of Targeted Therapy For Gastric Cancer, Andrew Tsourkas, Julie Czupryna Dec 2006

Suicide Gene Delivery By Calcium Phosphate Nanoparticles: A Novel Method Of Targeted Therapy For Gastric Cancer, Andrew Tsourkas, Julie Czupryna

Departmental Papers (BE)

No abstract provided.


Branching Pushdown Tree Automata, Rajeev Alur, Swarat Chaudhuri Dec 2006

Branching Pushdown Tree Automata, Rajeev Alur, Swarat Chaudhuri

Departmental Papers (CIS)

We observe that pushdown tree automata (PTAs) known in the literature cannot express combinations of branching and pushdown properties. This is because a PTA processes the children of a tree node in possibly different control states but with identical stacks. We propose branching pushdown tree automata (BPTAs) as a solution. In a BPTA, a push-move views its matching pops as an unbounded, unordered set of successor moves and can assert existential and universal requirements on them, just the way finite automata on unranked, unordered trees pass requirements to the children of a tree node. We show that BPTAs can express ...


Nosq: Store-Load Communication Without A Store Queue, Tingting Sha, Milo Martin, Amir Roth Dec 2006

Nosq: Store-Load Communication Without A Store Queue, Tingting Sha, Milo Martin, Amir Roth

Departmental Papers (CIS)

This paper presents NoSQ (short for No Store Queue), a microarchitecture that performs store-load communication without a store queue and without executing stores in the out-of-order engine. NoSQ implements store-load communication using speculative memory bypassing (SMB), the dynamic short-circuiting of DEF-store-load-USE chains to DEF-USE chains. Whereas previous proposals used SMB as an opportunistic complement to conventional store queue-based forwarding, NoSQ uses SMB as a store queue replacement.

NoSQ relies on two supporting mechanisms. The first is an advanced store-load bypassing predictor that for a given dynamic load can predict whether that load will bypass and the identity of the communicating ...


Cervical Facet Capsular Ligament Yield Defines The Threshold For Injury And Persistent Joint-Mediated Cervical Pain, Kyle P. Quinn, Beth A. Winkelstein Dec 2006

Cervical Facet Capsular Ligament Yield Defines The Threshold For Injury And Persistent Joint-Mediated Cervical Pain, Kyle P. Quinn, Beth A. Winkelstein

Departmental Papers (BE)

The cervical facet joint has been identified as a source of neck pain, and its capsular ligament is a likely candidate for injury during whiplash. Many studies have shown that the mechanical properties of ligaments can be altered by subfailure injury. However, the subfailure mechanical response of the facet capsular ligament has not been well defined, particularly in the context of physiology and pain. Therefore, the goal of this study was to quantify the structural mechanics of the cervical facet capsule and define the threshold for altered structural responses in this ligament during distraction. Tensile failure tests were preformed using ...


Spatial Grain Size Sorting In Eolian Ripples And Estimation Of Wind Conditions On Planetary Surfaces: Application To Meridiani Planum, Mars, Douglas J. Jerolmack, David Mohrig, John P. Grotzinger, David A. Fike, Wesley A. Watters Dec 2006

Spatial Grain Size Sorting In Eolian Ripples And Estimation Of Wind Conditions On Planetary Surfaces: Application To Meridiani Planum, Mars, Douglas J. Jerolmack, David Mohrig, John P. Grotzinger, David A. Fike, Wesley A. Watters

Departmental Papers (EES)

The landscape seen by the Mars Exploration Rover (MER) Opportunity at Meridiani Planum is dominated by eolian (wind-blown) ripples with concentrated surface lags of hematitic spherules and fragments. These ripples exhibit profound spatial grain size sorting, with well-sorted coarse-grained crests and poorly sorted, generally finer-grained troughs. These ripples were the most common bed form encountered by Opportunity in its traverse from Eagle Crater to Endurance Crater. Field measurements from White Sands National Monument, New Mexico, show that such coarse-grained ripples form by the different transport modes of coarse- and fine-grain fractions. On the basis of our field study, and simple ...


The Effect Of Ca-P Coated Bovine Bone Mineral On Bone Regeneration Around Dental Implant In Dogs, Su-Yeon Cho, Hyeran H. Jeon, Sun-Kyoung Lee, Seoung-Ho Lee, Jun-Young Lee, Keum-Ah Han Dec 2006

The Effect Of Ca-P Coated Bovine Bone Mineral On Bone Regeneration Around Dental Implant In Dogs, Su-Yeon Cho, Hyeran H. Jeon, Sun-Kyoung Lee, Seoung-Ho Lee, Jun-Young Lee, Keum-Ah Han

Departmental Papers (Dental)

There are many obstacles to overcome in implant dentistry. The bony defect around implant can be seen in immediate installation procedures. Following tooth extraction, however, a socket often presents dimensions that may be considerably greater than the dimensions of a conventional implant.


Robustness Analysis, Michael Weisberg Dec 2006

Robustness Analysis, Michael Weisberg

Departmental Papers (Philosophy)

Modelers often rely on robustness analysis, the search for predictions common to several independent models. Robustness analysis has been characterized and championed by Richard Levins and William Wimsatt, who see it as central to modern theoretical practice. The practice has also been severely criticized by Steven Orzack and Elliott Sober, who claim that it is a nonempirical form of confirmation, effective only under unusual circumstances. This paper addresses Orzack and Sober’s criticisms by giving a new account of robustness analysis and showing how the practice can identify robust theorems. Once the structure of robust theorems is clearly articulated, it ...


Neural Foundations To Moral Reasoning And Antisocial Behavior, Adrian Raine, Yaling Yang Dec 2006

Neural Foundations To Moral Reasoning And Antisocial Behavior, Adrian Raine, Yaling Yang

Neuroethics Publications

A common feature of the antisocial, rule-breaking behavior that is central to criminal, violent and psychopathic individuals is the failure to follow moral guidelines. This review summarizes key findings from brain imaging research on both antisocial behavior and moral reasoning, and integrates these findings into a neural moral model of antisocial behavior. Key areas found to be functionally or structurally impaired in antisocial populations include dorsal and ventral regions of the prefrontal cortex (PFC), amygdala, hippocampus, angular gyrus, anterior cingulate and temporal cortex. Regions most commonly activated in moral judgment tasks consist of the polar/medial and ventral PFC, amygdala ...


Why The Omega-3 Piggy Should Not Go To Market, Autumn Fiester Dec 2006

Why The Omega-3 Piggy Should Not Go To Market, Autumn Fiester

Center for Bioethics Papers

The paper in your April issue by Lai et al. entitled "Generation of cloned transgenic pigs rich in omega-3 fatty acids" (Nat. Biotechnol. 24, 435–436, 2006) perfectly captures the fundamental problem with American biotech research. That problem is that scientists pursue their research agenda to further scientific knowledge - all well and good - but when the project succeeds they invent problems for which their research results can be marketed as a solution. This unreflective move from 'pure science' to commercialization may end up as biotech's undoing.


Evaluating The Case Against Pet Cloning, Autumn Fiester Dec 2006

Evaluating The Case Against Pet Cloning, Autumn Fiester

Center for Bioethics Papers

The cause that opponents of pet cloning support is indisputably a worthy one: namely, the protection of animal welfare. And because this type of animal cloning appears, at least at first glance, to have no noble ends, the public and most animal ethicists have been content to let the cause, rather than the arguments, carry the day. There is an overwhelmingly negative view of companion animal cloning among the lay public, animal advocacy organizations, and professional ethicists. But how sound are their arguments against pet cloning? Can they withstand careful scrutiny?


Autocatalytic Activation Of Influenza Hemagglutinin, Jeong H. Lee, Mark Goulian, Eric T. Boder Dec 2006

Autocatalytic Activation Of Influenza Hemagglutinin, Jeong H. Lee, Mark Goulian, Eric T. Boder

Departmental Papers (CBE)

Enveloped viruses contain surface proteins that mediate fusion between the viral and target cell membranes following an activating stimulus. Acidic pH induces the influenza virus fusion protein hemagglutinin (HA) via irreversible refolding of a trimeric conformational state leading to exposure of hydrophobic fusion peptides on each trimer subunit. Herein, we show that cells expressing fowl plague virus HA demonstrate discrete switching behavior with respect to the HA conformational change. Partially activated states do not exist at the scale of the cell, activation of HA leads to aggregation of cell surface trimers, and newly synthesized HA refold spontaneously in the presence ...


Non-Interactive Correlation Distillation, Inhomogeneous Markov Chains, And The Reverse Bonami-Beckner Inequality, Elchanan Mossel, Ryan O'Donnell, Oded Regev, Jeffrey E. Steif, Benny Sudakov Dec 2006

Non-Interactive Correlation Distillation, Inhomogeneous Markov Chains, And The Reverse Bonami-Beckner Inequality, Elchanan Mossel, Ryan O'Donnell, Oded Regev, Jeffrey E. Steif, Benny Sudakov

Statistics Papers

In this paper we study non-interactive correlation distillation (NICD), a generalization of noise sensitivity previously considered in [5, 31, 39]. We extend the model toNICD on trees. In this model there is a fixed undirected tree with players at some of the nodes. One node is given a uniformly random string and this string is distributed throughout the network, with the edges of the tree acting as independent binary symmetric channels. The goal of the players is to agree on a shared random bit without communicating.

Our new contributions include the following: