Jerry Greenberg - Academia.edu (original) (raw)

Papers by Jerry Greenberg

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Gagan Agrawal Gabrielle Allen Gustavo Alonso Phil Andrews Cosimo Anglano Gabriel Antoniu Manish A... more Gagan Agrawal Gabrielle Allen Gustavo Alonso Phil Andrews Cosimo Anglano Gabriel Antoniu Manish Arora Laurent Baduel Joseph Bianco Rupak Biswas Todd Bryan Philip Buonadonna Henri Casanova DeQing Chen Kenneth Chiu Wahid Chrabakh Pérez Christian Morin Christine Brent Chun Giuseppe Ciaccio Arnaud Contes Balázs Csizmazia Steve Cutchin Karl Czajkowski Alexandre Denis Thomas Dramlitsch Torsten Fink Michail Flouris Brent Gorda Sergei Gorlatch ... Madhusudhan Govindaraju Ananth Grama Jerry Greenberg Anshul Gupta Daniel ...

Supercomputing Conference, 2002

High performance computing, storage, visualization, and database infrastructures are increasing g... more High performance computing, storage, visualization, and database infrastructures are increasing geometrically in complexity as scientists move towards grid-based computing. While this is natural, it has the effect of pushing computational capabilities beyond the reach of scientists because of the time needed to harness the infrastructure. Hiding the complexity of networked resources becomes essential if scientists are to utilize them effectively.

Lecture Notes in Computer Science, 2003

ABSTRACT We present a description of our ongoing efforts to utilize the services provided over th... more ABSTRACT We present a description of our ongoing efforts to utilize the services provided over the World Wide Web to advance the field of computational quantum chemistry utilized for detailed study of the electronic structure and properties of molecular systems, as well as the dissemination of results both for research and education. There are several facets of these efforts: (1) development of a computational chemistry web portal (2) development of an XML schema based on output data of electronic structure software, and (3) development of database and associated query tools that will serve as a basis for storage, retrieval, and manipulation of QM data in uniquely new ways. These efforts are distinctly coupled together through our creation of a “workflow” of web services, using grid resources.

ABSTRACT Utilization of computationally derived chemical and physical properties, in conjunction ... more ABSTRACT Utilization of computationally derived chemical and physical properties, in conjunction with experiments, has vastly enhanced the understanding of the properties of technologically important chemical structures. The application of computational techniques applied on the atomic scale such as a) the determination of reaction mechanisms, b) the study of the details of molecular forces and their role in structure determination, and c) the calculation of detailed potential energy surfaces and dynamics for reaction processes have led to advancements in areas such as materials chemistry, electronics, environmental chemistry, and medicinal chemistry. The ultimate goal of these calculations is the creation and understanding of ‘designer’ molecules that perform certain tasks within complex reaction chains and cycles. Because of the requirements that these types of molecular systems must display a special uniqueness of action or efficiency in response, the designer typically must meet strict criteria on specific structural tolerances. The resulting degree of complexity in these molecular blueprints increases at a rate only manageable by advanced high performance computing methods, such as massive parallelization, or ultrafast vectorization, as well as networked communications for data transfers.

Journal of bioinformatics and computational biology, 2008

Many major facilitator superfamily (MFS) transporters have similar 12-transmembrane alpha-helical... more Many major facilitator superfamily (MFS) transporters have similar 12-transmembrane alpha-helical topologies with two six-helix halves connected by a long loop. In humans, these transporters participate in key physiological processes and are also, as in the case of members of the organic anion transporter (OAT) family, of pharmaceutical interest. Recently, crystal structures of two bacterial representatives of the MFS family--the glycerol-3-phosphate transporter (GlpT) and lac-permease (LacY)--have been solved and, because of assumptions regarding the high structural conservation of this family, there is hope that the results can be applied to mammalian transporters as well. Based on crystallography, it has been suggested that a major conformational "switching" mechanism accounts for ligand transport by MFS proteins. This conformational switch would then allow periodic changes in the overall transporter configuration, resulting in its cyclic opening to the periplasm or cyt...

Journal of molecular graphics, 1996

The graphics program MDMovie (Molecular Dynamics Movie), written in C using IRIS GL graphics libr... more The graphics program MDMovie (Molecular Dynamics Movie), written in C using IRIS GL graphics library calls, is designed to facilitate the visualization and interpretation of empirical force field data. MDMovie was created and initially adapted in accord with the needs of physical chemists and thereafter became an expandable analysis tool. Capabilities include the display of chemical structure, animation of molecular dynamics and Monte Carlo trajectories, and the visual representation of various vector and scalar dynamical properties. In addition to being a research tool, MDMovie has features for creating presentation videos and hardcopy output. A library is also available for linking to Fortran simulation codes running on a remote machine and connecting to MDMovie via a socket connection. MDMovie continues to be an ongoing research project and new features are actively being added in collaboration with various research groups. Future plans include porting to OpenGL and the design of...

Models, Enabling Technologies, and Case Studies, 2005

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Journal of molecular graphics, 1995

QMView is designed to facilitate the visualization and interpretation of quantum mechanical data.... more QMView is designed to facilitate the visualization and interpretation of quantum mechanical data. Capabilities include display of chemical structure, animation of quantum mechanically determined vibrational modes, and depiction of electronic properties and three-dimensional molecular orbitals. QMView has a user-friendly interface that allows users to interactively manipulate many features of the molecular structure and/or property, including positioning and structure representation, via mouse-activated dialog boxes. Although the interface allows input from results of any of the popularly used quantum mechanical software, we have focused on GAMESS, a widely distributed quantum chemistry code. QMView has been designed with the special feature of working in distributed mode with GAMESS, the latter running on a supercomputer, the former running on a Silicon Graphics platform. Ancillary programs provide a method of obtaining output of graphic images in various media, including hardcopy, ...

Oncotarget, Jan 28, 2015

We hypothesized that aberrations activating epidermal growth factor receptor (EGFR) via dimerizat... more We hypothesized that aberrations activating epidermal growth factor receptor (EGFR) via dimerization would be more sensitive to anti-dimerization agents (e.g., cetuximab). EGFR exon 19 abnormalities (L747_A750del; deletes amino acids LREA) respond to reversible EGFR kinase inhibitors (TKIs). Exon 20 in-frame insertions and/or duplications (codons 767 to 774) and T790M mutations are clinically resistant to reversible/some irreversible TKIs. Their impact on protein function/therapeutic actionability are not fully elucidated.In our study, the index patient with non-small cell lung cancer (NSCLC) harbored EGFR D770_P772del_insKG (exon 20). A twenty patient trial (NSCLC cohort) (cetuximab-based regimen) included two participants with EGFR TKI-resistant mutations ((i) exon 20 D770>GY; and (ii) exon 19 LREA plus exon 20 T790M mutations). Structural modeling predicted that EGFR exon 20 anomalies (D770_P772del_insKG and D770>GY), but not T790M mutations, stabilize the active dimer conf...

The UCSD brine chemistry program is providing highly accurate models of the behavior of high temp... more The UCSD brine chemistry program is providing highly accurate models of the behavior of high temperature brines to be used by the geothermal community to optimize production, interpret formation behavior and assist in performance assessment. Models are now available as user-oriented programs packaged for both main frame and personal computers (IBM and Macintosh). A manual describing the models and their

Journal of Alzheimer's disease : JAD, 2014

Alzheimer's disease (AD) is associated with the formation of toxic amyloid-β (Aβ)42 oligomers... more Alzheimer's disease (AD) is associated with the formation of toxic amyloid-β (Aβ)42 oligomers, and recent evidence supports a role for Aβ dimers as building blocks for oligomers. Molecular dynamics simulation studies have identified clans for the dominant conformations of Aβ42 forming dimers; however, it is unclear if a larger spectrum of dimers is involved and which set(s) of dimers might evolve to oligomers verse fibrils. Therefore, for this study we generated multiple structural conformations of Aβ42, using explicit all-atom molecular dynamics, and then clustering the different structures based on key conformational similarities. Those matching a selection threshold were then used to model a process of oligomerization. Remarkably, we showed a greater diversity in Aβ dimers than previously described. Depending on the clan family, different types of Aβ dimers were obtained. While some had the tendency to evolve into oligomeric rings, others formed fibrils of diverse characteris...

Proceedings of the Conference on Extreme Science and Engineering Discovery Environment Gateway to Discovery - XSEDE '13, 2013

ABSTRACT The Hadoop framework is extensively used for scalable distributed processing of large da... more ABSTRACT The Hadoop framework is extensively used for scalable distributed processing of large datasets. This extended abstract provides information on the optimization of the Hadoop deployment on the Gordon data intensive supercomputer, at the San Diego Supercomputer Center (SDSC) at the University of California San Diego, using the myHadoop software. The details of the system configuration, the storage and network options (1 Gig-E, IPOIB, and UDA), tuning options considered, results using the TestDFSIO, TeraSort benchmarks, and bulk copy tests with distcp are presented in this extended abstract.

ACS Chemical Neuroscience, 2015

Parkinson's disease (PD) is associated with the formation of toxic α-synuclein oligomers that can... more Parkinson's disease (PD) is associated with the formation of toxic α-synuclein oligomers that can penetrate the cell membrane. Familial forms of PD are caused by the point mutations A53T, A30P, E46K, and H50Q. Artificial point mutations E35K and E57K also increase oligomerization and pore formation. We generated structural conformations of α-synuclein and the above-mentioned mutants using molecular dynamics. We elucidated four main regions in these conformers contacting the membrane and found that the region including residues 39−45 (Zone2) may have maximum membrane penetration. E57K mutant had the highest rate of interaction with the membrane, followed by A53T, E46K, and E35K mutants and wild type (wt) α-synuclein. The mutant A30P had the smallest percentage of conformers that contact the membrane by Zone 2 than all other mutants and wt α-synuclein. These results were confirmed experimentally in vitro. We identified the key amino acids that can interact with the membrane (Y38, E62, and N65 (first hydrophilic layer); E104, E105, and D115 (second hydrophilic layer), and V15 and V26 (central hydrophobic layer)) and the residues that are involved in the interprotein contacts (L38, V48, V49, Q62, and T64). Understanding the molecular interactions of α-synuclein mutants is important for the design of compounds blocking the formation of toxic oligomers.

Supramolecular Stereochemistry, 1995

Transport in porous media, 1998

... They also have wide applications in other industries (eg chemical processes, stripping tower ... more ... They also have wide applications in other industries (eg chemical processes, stripping tower design, solar pond engineering, waste isolation) and geochemical studies (see, for example, Harvie et al., 1980, 1984; Brantley et al., 1984; Felmy and Weare, 1986; Moller, 1988 ...

Journal of Chemical & Engineering Data, 1979

Geothermics, 1986

ABSTRACT Problems associated with the manipulation of highly concentrated brines at high temperat... more ABSTRACT Problems associated with the manipulation of highly concentrated brines at high temperatures have severely hindered the development of important geothermal energy resources in the Imperial Valley of Southern California and in other locations. One of the most serious of these problems is the precipitation of various mineral phases when the working fluid becomes supersaturated due to changes in external pressure or temperature. Scaling in well bores can significantly diminish flow rates and eventually seal the well. Precipitation of minerals in the energy production plant can cause costly downtimes in order to remove scales from the operating equipment. Similar chemical problems arise when spent geothermal brines are injected into an incompatible mineral formation. In this report we describe a chemical model which accurately predicts the properties of geothermal brines.