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Dartmouth College

2005

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Articles 61 - 73 of 73

Full-Text Articles in Physical Sciences and Mathematics

Graphical Models Of Residue Coupling In Protein Families, John Thomas, Naren Ramakrishnan, Chris Bailey-Kellogg Mar 2005

Graphical Models Of Residue Coupling In Protein Families, John Thomas, Naren Ramakrishnan, Chris Bailey-Kellogg

Computer Science Technical Reports

Identifying residue coupling relationships within a protein family can provide important insights into intrinsic molecular processes, and has significant applications in modeling structure and dynamics, understanding function, and designing new or modified proteins. We present the first algorithm to infer an undirected graphical model representing residue coupling in protein families. Such a model serves as a compact description of the joint amino acid distribution, and can be used for predictive (will this newly designed protein be folded and functional?), diagnostic (why is this protein not stable or functional?), and abductive reasoning (what if I attempt to graft features of one …

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Secure Context-Sensitive Authorization, Kazuhiro Minami, David Kotz Mar 2005

Secure Context-Sensitive Authorization, Kazuhiro Minami, David Kotz

Dartmouth Scholarship

There is a recent trend toward rule-based authorization systems to achieve flexible security policies. Also, new sensing technologies in pervasive computing make it possible to define context-sensitive rules, such as “allow database access only to staff who are currently located in the main office.” However, these rules, or the facts that are needed to verify authority, often involve sensitive context information. This paper presents a secure context-sensitive authorization system that protects confidential information in facts or rules. Furthermore, our system allows multiple hosts in a distributed environment to perform the evaluation of an authorization query in a collaborative way; we …

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Policy-Driven Data Dissemination For Context-Aware Applications, Guanling Chen, David Kotz Mar 2005

Policy-Driven Data Dissemination For Context-Aware Applications, Guanling Chen, David Kotz

Dartmouth Scholarship

Context-aware pervasive-computing applications require continuous monitoring of their physical and computational environment to make appropriate adaptation decisions in time. The data streams produced by sensors, however, may overflow the queues on the dissemination path. Traditional flow-control and congestion-control policies either drop data or force the sender to pause. When the data sender is sensing the physical environment, however, a pause is equivalent to dropping data. Instead of arbitrarily dropping data that may contain important events, we present a policy-driven data dissemination service named PACK, based on an overlay-based infrastructure for efficient multicast delivery. PACK enforces application-specified policies that define how …

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Shemp: Secure Hardware Enhanced Myproxy, John Marchesini, Sean Smith Feb 2005

Shemp: Secure Hardware Enhanced Myproxy, John Marchesini, Sean Smith

Computer Science Technical Reports

While PKI applications differ in how they use keys, all applications share one assumption: users have keypairs. In previous work, we established that desktop keystores are not safe places to store private keys, because the TCB is too large. These keystores are also immobile, difficult to use, and make it impossible for relying parties to make reasonable trust judgments. Since we would like to use desktops as PKI clients and cannot realistically expect to redesign the entire desktop, this paper presents a system that works within the confines of modern desktops to shrink the TCB needed for PKI applications. Our …

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Creep Of Granular Ice With And Without Dispersed Particles, Min Song, David M. Cole, Ian Baker Jan 2005

Creep Of Granular Ice With And Without Dispersed Particles, Min Song, David M. Cole, Ian Baker

Dartmouth Scholarship

The effects of silt-sized particles (average diameter of 50 m m) on the compressive creep of polycrystalline ice have been studied at stress levels from 0.1 to 1.45MPa and temperatures of –12 8 C and –10 8 C. Dislocation densities during creep have been estimated using a dislocation-based model of anelasticity. The results indicate that at low concentrations (up to 4wt.% % ), particles increase the minimum creep rate. Power-law behavior with an exponent of 3 was observed for both particle-free ice and ice with 1 wt.% % particles when the stress was >0.3 MPa. In contrast, linear behavior was …

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Ultrarelativistic Plasma Shell Collisions In Γ‐Ray Burst Sources: Dimensional Effects On The Final Steady State Magnetic Field, C. H. Jaroschek, H. Lesch, R. A. Treumann Jan 2005

Ultrarelativistic Plasma Shell Collisions In Γ‐Ray Burst Sources: Dimensional Effects On The Final Steady State Magnetic Field, C. H. Jaroschek, H. Lesch, R. A. Treumann

Dartmouth Scholarship

Ultrarelativistic electron-positron plasma shell collisions as an integral part of generic γ-ray burst (GRB) fireball models are studied in the framework of self-consistent three-dimensional particle-in-cell simulations. We compare scenarios at moderately relativistic (γ0 10) and ultrarelativistic (γ0 100) energies that directly correspond to the regimes of internal and external shell collisions, respectively, in GRB synchrotron emission models. Simulated systems comprise 5 × 108 particles, applying a relativistic, fully electromagnetic, massively parallelized code. It is found that Weibel-generated, steady state magnetic equipartition ratios in external collisions reach up to B ~ 12%, exceeding the respective internal ratios by …

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High-Throughput Inference Of Protein-Protein Interaction Sites From Unassigned Nmr Data By Analyzing Arrangements Induced By Quadratic Forms On 3-Manifolds, Ramgopal R. Mettu, Ryan H. Lilien, Bruce Randall Donald Jan 2005

High-Throughput Inference Of Protein-Protein Interaction Sites From Unassigned Nmr Data By Analyzing Arrangements Induced By Quadratic Forms On 3-Manifolds, Ramgopal R. Mettu, Ryan H. Lilien, Bruce Randall Donald

Computer Science Technical Reports

We cast the problem of identifying protein-protein interfaces, using only unassigned NMR spectra, into a geometric clustering problem. Identifying protein-protein interfaces is critical to understanding inter- and intra-cellular communication, and NMR allows the study of protein interaction in solution. However it is often the case that NMR studies of a protein complex are very time-consuming, mainly due to the bottleneck in assigning the chemical shifts, even if the apo structures of the constituent proteins are known. We study whether it is possible, in a high-throughput manner, to identify the interface region of a protein complex using only unassigned chemical shift …

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Microstructural Characterization Of Ice Cores, Ian Baker, Daniel Iliescu, Rachel Obbard, Hui Chang, Benjamin Bostick, Charles Daghlian Jan 2005

Microstructural Characterization Of Ice Cores, Ian Baker, Daniel Iliescu, Rachel Obbard, Hui Chang, Benjamin Bostick, Charles Daghlian

Dartmouth Scholarship

No abstract provided.

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Knowing When To Draw The Line: Designing More Informative Ecological Experiments, Kathryn L. Cottingham, Jay T. Lennon, Bryan L. Brown Jan 2005

Knowing When To Draw The Line: Designing More Informative Ecological Experiments, Kathryn L. Cottingham, Jay T. Lennon, Bryan L. Brown

Dartmouth Scholarship

Linear regression and analysis of variance (ANOVA) are two of the most widely used statistical techniques in ecology. Regression quantitatively describes the relationship between a response variable and one or more continuous independent variables, while ANOVA determines whether a response variable differs among discrete values of the independent variable(s). Designing experiments with discrete factors is straightforward because ANOVA is the only option, but what is the best way to design experiments involving continuous factors? Should ecologists prefer experiments with few treatments and many replicates analyzed with ANOVA, or experiments with many treatments and few replicates per treatment analyzed with regression? …

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Spectroscopy Of Kiss Emission-Line Galaxy Candidates. Iii. A Second Set Of Mdm Observations, Anna Jangren, Gary Wegner, John J. Salzer, Jessica K. Werk, Caryl Gronwall Jan 2005

Spectroscopy Of Kiss Emission-Line Galaxy Candidates. Iii. A Second Set Of Mdm Observations, Anna Jangren, Gary Wegner, John J. Salzer, Jessica K. Werk, Caryl Gronwall

Dartmouth Scholarship

Spectroscopic observations for 315 emission-line galaxy (ELG) candidates from the KPNO International Spectroscopic Survey (KISS) have been obtained using the MDM Observatory 2.4 m telescope on Kitt Peak. KISS is a wide-field objective-prism survey for extragalactic emission-line objects that has cataloged over 2200 ELG candidates to date. Spectroscopic follow-up observations are being carried out to study the characteristics of the survey objects. The observational data presented here include redshifts, reddening estimates, line equivalent widths, Hα line fluxes, and emission-line ratios. The galaxies have been classified based on their emission-line characteristics. The procedure for selecting the ELG candidates in KISS is …

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Synthetic Studies In Phytochrome Chemistry, Peter A. Jacobi, Imad Odeh, Subhas Buddhu, Guolin Cai, Sundaramoorthi Rajeswari, Douglas Fry, Wanjun Zheng, Robert W. Desimone, Jiasheng Guo, Lisa D. Coutts, Sheila I. Hauck, Sam H. Leung, Indranath Ghosh, Douglas Pippin Jan 2005

Synthetic Studies In Phytochrome Chemistry, Peter A. Jacobi, Imad Odeh, Subhas Buddhu, Guolin Cai, Sundaramoorthi Rajeswari, Douglas Fry, Wanjun Zheng, Robert W. Desimone, Jiasheng Guo, Lisa D. Coutts, Sheila I. Hauck, Sam H. Leung, Indranath Ghosh, Douglas Pippin

Dartmouth Scholarship

An account is given of the author’s several approaches to the synthesis of the parent chromophore of phytochrome (1), a protein-bound linear tetrapyrrole derivative that controls photomorphogenesis in higher plants. These studies culminated in enantioselective syntheses of both (2R)- and (2S)-phytochromobilin (4), as well as several 13C-labeled derivatives designed to probe the site of Z,E-isomerization during photoexcitation. When reacted in vitro, synthetic 2R-4 and recombinant-derived phytochrome apoprotein N-C produced a protein-bound chromophore with identical difference spectra to naturally occurring 1.

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The Kerf Toolkit For Intrusion Analysis, Javed Aslam, Sergey Bratus, David Kotz, Ronald Peterson Jan 2005

The Kerf Toolkit For Intrusion Analysis, Javed Aslam, Sergey Bratus, David Kotz, Ronald Peterson

Dartmouth Scholarship

No abstract provided.

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Crystal Structure Of The Gtpase Domain Of Rat Dynamin 1, Thomas F. Reubold, Susanne Eschenburg, Andreas Becker, Marilyn Leonard, Sandra L. Schmid, Richard B. Vallee, F. Jon Kull, Dietmar J. Manstein Jan 2005

Crystal Structure Of The Gtpase Domain Of Rat Dynamin 1, Thomas F. Reubold, Susanne Eschenburg, Andreas Becker, Marilyn Leonard, Sandra L. Schmid, Richard B. Vallee, F. Jon Kull, Dietmar J. Manstein

Dartmouth Scholarship

Here, we present the 1.9-A crystal structure of the nucleotide-free GTPase domain of dynamin 1 from Rattus norvegicus. The structure corresponds to an extended form of the canonical GTPase fold observed in Ras proteins. Both nucleotide-binding switch motifs are well resolved, adopting conformations that closely resemble a GTP-bound state not previously observed for nucleotide-free GTPases. Two highly conserved arginines, Arg-66 and Arg-67, greatly restrict the mobility of switch I and are ideally positioned to relay information about the nucleotide state to other parts of the protein. Our results support a model in which switch I residue Arg-59 gates GTP binding …

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