Search Results - "Barnes, George L"

tsscds2018: A code for automated discovery of chemical reaction mechanisms and solving the kinetics by Rodríguez, Aurelio, Rodríguez-Fernández, Roberto, A Vázquez, Saulo, L Barnes, George, J P Stewart, James, Martínez-Núñez, Emilio

“…A new software, called tsscds2018, has been developed to discover reaction mechanisms and solve the kinetics in a fully automated fashion. The program employs…”
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The VENUS/NWChem software package. Tight coupling between chemical dynamics simulations and electronic structure theory by Lourderaj, Upakarasamy, Sun, Rui, Kohale, Swapnil C., Barnes, George L., de Jong, Wibe A., Windus, Theresa L., Hase, William L.

“…The interface for VENUS and NWChem, and the resulting software package for direct dynamics simulations are described. The coupling of the two codes is…”
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Fracture healing as a post-natal developmental process: Molecular, spatial, and temporal aspects of its regulation by Gerstenfeld, Louis C., Cullinane, Dennis M., Barnes, George L., Graves, Dana T., Einhorn, Thomas A.

“…Fracture healing is a specialized post‐natal repair process that recapitulates aspects of embryological skeletal development. While many of the molecular…”
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Micro-computed tomography assessment of fracture healing: Relationships among callus structure, composition, and mechanical function by Morgan, Elise F, Mason, Zachary D, Chien, Karen B, Pfeiffer, Anthony J, Barnes, George L, Einhorn, Thomas A, Gerstenfeld, Louis C

“…Abstract Non-invasive characterization of fracture callus structure and composition may facilitate development of surrogate measures of the regain of…”
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Enhanced Chondrogenesis and Wnt Signaling in PTH‐Treated Fractures by Kakar, Sanjeev, Einhorn, Thomas A, Vora, Siddharth, Miara, Lincoln J, Hon, Gregory, Wigner, Nathan A, Toben, Daniel, Jacobsen, Kimberly A, Al‐Sebaei, Maisa O, Song, Michael, Trackman, Philip C, Morgan, Elise F, Gerstenfeld, Louis C, Barnes, George L

“…Studies have shown that systemic PTH treatment enhanced the rate of bone repair in rodent models. However, the mechanisms through which PTH affects bone repair…”
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Osteogenic differentiation of marrow stromal cells cultured on nanoporous alumina surfaces by Popat, Ketul C., Chatvanichkul, Kwan-Isara, Barnes, George L., Latempa Jr, Thomas Joseph, Grimes, Craigs A., Desai, Tejal A.

“…A major goal in orthopedic biomaterials research is to design implant surfaces, which will enhance osseointegration in vivo. Several microscale as well as…”
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Impaired Intranuclear Trafficking of Runx2 (AML3/CBFA1) Transcription Factors in Breast Cancer Cells Inhibits Osteolysis in vivo by Javed, Amjad, Barnes, George L., Pratap, Jitesh, Antkowiak, Tomasz, Gerstenfeld, Louis C., van Wijnen, Andre J., Stein, Janet L., Lian, Jane B., Stein, Gary S., Penman, Sheldon

“…Runx transcription factors comprise a family of proteins that are essential for organogenesis. A unique nuclear matrix-targeting signal in the C terminus…”
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Direct Chemical Dynamics Simulations by Pratihar, Subha, Ma, Xinyou, Homayoon, Zahra, Barnes, George L, Hase, William L

“…In a direct dynamics simulation, the technologies of chemical dynamics and electronic structure theory are coupled so that the potential energy, gradient, and…”
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Fidelity of Runx2 activity in breast cancer cells is required for the generation of metastases-associated osteolytic disease by BARNES, George L, HEBERT, Kerri E, KAMAL, Mohammad, JAVED, Amjad, EINHORN, Thomas A, LIAN, Jane B, STEIN, Gary S, GERSTENFELD, Louis C

“…The osteolytic bone destruction associated with breast cancer skeletal metastases represents a serious and incurable clinical condition. However, the molecular…”
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Modeling the Effects of O‑Sulfonation on the CID of Serine by Lucas, Kenneth, Barnes, George L

“…We present the results of direct dynamics simulations and DFT calculations aimed at elucidating the effect of O-sulfonation on the collision-induced…”
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A Computational Comparison of Soft Landing of α‑Helical vs Globular Peptides by Frederickson, Danielle, McDonough, Meghan, Barnes, George L

“…The effect of secondary structure on the soft landing process is investigated through direct dynamics simulations of AcA7K and AcKA7 colliding with a…”
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Simulating the Effect of Charge State on Reactive Landing of a Cyclic Tetrapeptide on Chemically Modified Alkylthiolate Self-Assembled Monolayer Surfaces by Barnes, George L, Podczerwinski, Amanda

“…Previous simulations have provided insight into reactive landing (RL) of protonated peptides on chemically modified organic self-assembled monolayer (SAM)…”
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Chemical dynamics simulations of energy transfer, surface-induced dissociation, soft-landing, and reactive-landing in collisions of protonated peptide ions with organic surfaces by Pratihar, Subha, Barnes, George L, Hase, William L

“…There are two components to the review presented here regarding simulations of collisions of protonated peptide ions peptide-H(+) with organic surfaces. One is…”
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AutoMeKin2021: An open‐source program for automated reaction discovery by Martínez‐Núñez, Emilio, Barnes, George L., Glowacki, David R., Kopec, Sabine, Peláez, Daniel, Rodríguez, Aurelio, Rodríguez‐Fernández, Roberto, Shannon, Robin J., Stewart, James J. P., Tahoces, Pablo G., Vazquez, Saulo A.

“…AutoMeKin2021 is an updated version of tsscds2018, a program for the automated discovery of reaction mechanisms (J. Comput. Chem. 2018, 39, 1922). This release…”
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Dynamics of Protonated Peptide Ion Collisions with Organic Surfaces: Consonance of Simulation and Experiment by Pratihar, Subha, Barnes, George L, Laskin, Julia, Hase, William L

“…In this Perspective, mass spectrometry experiments and chemical dynamics simulations are described that have explored the atomistic dynamics of protonated…”
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Memorial Viewpoint for William L. Hase by Lischka, Hans, Tully, John, Wang, Haobin, Barnes, George L

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Exploring the Effects of Methylation on the CID of Protonated Lysine: A Combined Experimental and Computational Approach by Lucas, Kenneth, Chen, Amy, Schubmehl, Megan, Kolonko, Kristopher J, Barnes, George L

“…We report the results of experiments, simulations, and DFT calculations that focus on describing the reaction dynamics observed within the collision-induced…”
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Model Simulations of the Thermal Dissociation of the TIK(H+)2 Tripeptide: Mechanisms and Kinetic Parameters by Homayoon, Zahra, Pratihar, Subha, Dratz, Edward, Snider, Ross, Spezia, Riccardo, Barnes, George L, Macaluso, Veronica, Martin Somer, Ana, Hase, William L

“…Direct dynamics simulations, utilizing the RM1 semiempirical electronic structure theory, were performed to study the thermal dissociation of the doubly…”
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Role of Chemical Dynamics Simulations in Mass Spectrometry Studies of Collision-Induced Dissociation and Collisions of Biological Ions with Organic Surfaces by Martin Somer, Ana, Macaluso, Veronica, Barnes, George L, Yang, Li, Pratihar, Subha, Song, Kihyung, Hase, William L, Spezia, Riccardo

“…In this article, a perspective is given of chemical dynamics simulations of collisions of biological ions with surfaces and of collision-induced dissociation…”
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Complex Formation during SID and Its Effect on Proton Mobility by Ijaz, Waleed, Gregg, Zackary, Barnes, George L

“…Surface-induced dissociation (SID) of protonated peptides is a vibrant, active field of study. Significant focus has been placed on understanding the mechanism…”
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