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Showing 1 to 12 of 168 entries
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High-Pressure NiAs-Type Modification of FeN.

Angewandte Chemie (International ed. in English)

Clark WP, Steinberg S, Dronskowski R, McCammon C, Kupenko I, Bykov M, Dubrovinsky L, Akselrud LG, Schwarz U, Niewa R.
PMID: 28517174
Angew Chem Int Ed Engl. 2017 Jun 12;56(25):7302-7306. doi: 10.1002/anie.201702440. Epub 2017 May 18.

The combination of laser-heated diamond anvil cells and synchrotron Mössbauer source spectroscopy were used to investigate high-temperature high-pressure chemical reactions of iron and iron nitride Fe

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Clark WP, Steinberg S, Dronskowski R, et al. High-Pressure NiAs-Type Modification of FeN. Angew Chem Int Ed Engl. 2017;56(25):7302-7306doi: 10.1002/anie.201702440.
Clark, W. P., Steinberg, S., Dronskowski, R., McCammon, C., Kupenko, I., Bykov, M., Dubrovinsky, L., Akselrud, L. G., Schwarz, U., & Niewa, R. (2017). High-Pressure NiAs-Type Modification of FeN. Angewandte Chemie (International ed. in English), 56(25), 7302-7306. https://doi.org/10.1002/anie.201702440
Clark, William P, et al. "High-Pressure NiAs-Type Modification of FeN." Angewandte Chemie (International ed. in English) vol. 56,25 (2017): 7302-7306. doi: https://doi.org/10.1002/anie.201702440
Clark WP, Steinberg S, Dronskowski R, McCammon C, Kupenko I, Bykov M, Dubrovinsky L, Akselrud LG, Schwarz U, Niewa R. High-Pressure NiAs-Type Modification of FeN. Angew Chem Int Ed Engl. 2017 Jun 12;56(25):7302-7306. doi: 10.1002/anie.201702440. Epub 2017 May 18. PMID: 28517174; PMCID: PMC5488211.
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Hybrid finite element and Brownian dynamics method for charged particles.

The Journal of chemical physics

Huber GA, Miao Y, Zhou S, Li B, McCammon JA.
PMID: 27131531
J Chem Phys. 2016 Apr 28;144(16):164107. doi: 10.1063/1.4947086.

Diffusion is often the rate-determining step in many biological processes. Currently, the two main computational methods for studying diffusion are stochastic methods, such as Brownian dynamics, and continuum methods, such as the finite element method. A previous study introduced...

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Huber GA, Miao Y, Zhou S, et al. Hybrid finite element and Brownian dynamics method for charged particles. J Chem Phys. 2016;144(16):164107doi: 10.1063/1.4947086.
Huber, G. A., Miao, Y., Zhou, S., Li, B., & McCammon, J. A. (2016). Hybrid finite element and Brownian dynamics method for charged particles. The Journal of chemical physics, 144(16), 164107. https://doi.org/10.1063/1.4947086
Huber, Gary A, et al. "Hybrid finite element and Brownian dynamics method for charged particles." The Journal of chemical physics vol. 144,16 (2016): 164107. doi: https://doi.org/10.1063/1.4947086
Huber GA, Miao Y, Zhou S, Li B, McCammon JA. Hybrid finite element and Brownian dynamics method for charged particles. J Chem Phys. 2016 Apr 28;144(16):164107. doi: 10.1063/1.4947086. PMID: 27131531; PMCID: PMC4851620.
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Optimized Radii for Poisson-Boltzmann Calculations with the AMBER Force Field.

Journal of chemical theory and computation

Swanson JM, Adcock SA, McCammon JA.
PMID: 26641515
J Chem Theory Comput. 2005 May;1(3):484-93. doi: 10.1021/ct049834o.

Implicit solvent models are a standard tool for assessing the electrostatics of biomolecular systems. The accuracy of quantitative predictions, such as pKa values, transfer free energies, binding energies, and solvation forces, is strongly dependent on one's choice of continuum...

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Swanson JM, Adcock SA, McCammon JA. Optimized Radii for Poisson-Boltzmann Calculations with the AMBER Force Field. J Chem Theory Comput. 2005;1(3):484-93doi: 10.1021/ct049834o.
Swanson, J. M., Adcock, S. A., & McCammon, J. A. (2005). Optimized Radii for Poisson-Boltzmann Calculations with the AMBER Force Field. Journal of chemical theory and computation, 1(3), 484-93. https://doi.org/10.1021/ct049834o
Swanson, Jessica M J, et al. "Optimized Radii for Poisson-Boltzmann Calculations with the AMBER Force Field." Journal of chemical theory and computation vol. 1,3 (2005): 484-93. doi: https://doi.org/10.1021/ct049834o
Swanson JM, Adcock SA, McCammon JA. Optimized Radii for Poisson-Boltzmann Calculations with the AMBER Force Field. J Chem Theory Comput. 2005 May;1(3):484-93. doi: 10.1021/ct049834o. PMID: 26641515.
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Expenditures in the elderly with peripheral neuropathy: Where should we focus cost-control efforts?.

Neurology. Clinical practice

Callaghan BC, Burke JF, Rodgers A, McCammon R, Langa KM, Feldman EL, Kerber KA.
PMID: 24175158
Neurol Clin Pract. 2013 Oct;3(5):421-430. doi: 10.1212/CPJ.0b013e3182a78fb1.

To optimize care in the evaluation of peripheral neuropathy, we sought to define which tests drive expenditures and the role of the provider type. We investigated test utilization and expenditures by provider type in those with incident neuropathy in...

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Callaghan BC, Burke JF, Rodgers A, et al. Expenditures in the elderly with peripheral neuropathy: Where should we focus cost-control efforts?. Neurol Clin Pract. 2013;3(5):421-430doi: 10.1212/CPJ.0b013e3182a78fb1.
Callaghan, B. C., Burke, J. F., Rodgers, A., McCammon, R., Langa, K. M., Feldman, E. L., & Kerber, K. A. (2013). Expenditures in the elderly with peripheral neuropathy: Where should we focus cost-control efforts?. Neurology. Clinical practice, 3(5), 421-430. https://doi.org/10.1212/CPJ.0b013e3182a78fb1
Callaghan, Brian C, et al. "Expenditures in the elderly with peripheral neuropathy: Where should we focus cost-control efforts?." Neurology. Clinical practice vol. 3,5 (2013): 421-430. doi: https://doi.org/10.1212/CPJ.0b013e3182a78fb1
Callaghan BC, Burke JF, Rodgers A, McCammon R, Langa KM, Feldman EL, Kerber KA. Expenditures in the elderly with peripheral neuropathy: Where should we focus cost-control efforts?. Neurol Clin Pract. 2013 Oct;3(5):421-430. doi: 10.1212/CPJ.0b013e3182a78fb1. PMID: 24175158; PMCID: PMC3806930.
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Variational Implicit Solvation with Poisson-Boltzmann Theory.

Journal of chemical theory and computation

Zhou S, Cheng LT, Dzubiella J, Li B, McCammon JA.
PMID: 24803864
J Chem Theory Comput. 2014 Apr 08;10(4):1454-1467. doi: 10.1021/ct401058w. Epub 2014 Feb 21.

We incorporate the Poisson-Boltzmann (PB) theory of electrostatics into our variational implicit-solvent model (VISM) for the solvation of charged molecules in an aqueous solvent. In order to numerically relax the VISM free-energy functional by our level-set method, we develop...

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Zhou S, Cheng LT, Dzubiella J, et al. Variational Implicit Solvation with Poisson-Boltzmann Theory. J Chem Theory Comput. 2014;10(4):1454-1467doi: 10.1021/ct401058w.
Zhou, S., Cheng, L. T., Dzubiella, J., Li, B., & McCammon, J. A. (2014). Variational Implicit Solvation with Poisson-Boltzmann Theory. Journal of chemical theory and computation, 10(4), 1454-1467. https://doi.org/10.1021/ct401058w
Zhou, Shenggao, et al. "Variational Implicit Solvation with Poisson-Boltzmann Theory." Journal of chemical theory and computation vol. 10,4 (2014): 1454-1467. doi: https://doi.org/10.1021/ct401058w
Zhou S, Cheng LT, Dzubiella J, Li B, McCammon JA. Variational Implicit Solvation with Poisson-Boltzmann Theory. J Chem Theory Comput. 2014 Apr 08;10(4):1454-1467. doi: 10.1021/ct401058w. Epub 2014 Feb 21. PMID: 24803864; PMCID: PMC3985794.
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Computing the Amino Acid Specificity of Fluctuations in Biomolecular Systems.

Journal of chemical theory and computation

Hamacher K, McCammon JA.
PMID: 26626694
J Chem Theory Comput. 2006 May;2(3):873-8. doi: 10.1021/ct050247s.

We developed a new amino acid specific method for the computation of spatial fluctuations of proteins around their native structures. We show the consistency with experimental values and the increased performance in comparison to an established model, based on...

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Hamacher K, McCammon JA. Computing the Amino Acid Specificity of Fluctuations in Biomolecular Systems. J Chem Theory Comput. 2006;2(3):873-8doi: 10.1021/ct050247s.
Hamacher, K., & McCammon, J. A. (2006). Computing the Amino Acid Specificity of Fluctuations in Biomolecular Systems. Journal of chemical theory and computation, 2(3), 873-8. https://doi.org/10.1021/ct050247s
Hamacher, K, and McCammon, J A. "Computing the Amino Acid Specificity of Fluctuations in Biomolecular Systems." Journal of chemical theory and computation vol. 2,3 (2006): 873-8. doi: https://doi.org/10.1021/ct050247s
Hamacher K, McCammon JA. Computing the Amino Acid Specificity of Fluctuations in Biomolecular Systems. J Chem Theory Comput. 2006 May;2(3):873-8. doi: 10.1021/ct050247s. PMID: 26626694.
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Improved Reweighting of Accelerated Molecular Dynamics Simulations for Free Energy Calculation.

Journal of chemical theory and computation

Miao Y, Sinko W, Pierce L, Bucher D, Walker RC, McCammon JA.
PMID: 25061441
J Chem Theory Comput. 2014 Jul 08;10(7):2677-2689. doi: 10.1021/ct500090q. Epub 2014 May 01.

Accelerated molecular dynamics (aMD) simulations greatly improve the efficiency of conventional molecular dynamics (cMD) for sampling biomolecular conformations, but they require proper reweighting for free energy calculation. In this work, we systematically compare the accuracy of different reweighting algorithms...

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Miao Y, Sinko W, Pierce L, et al. Improved Reweighting of Accelerated Molecular Dynamics Simulations for Free Energy Calculation. J Chem Theory Comput. 2014;10(7):2677-2689doi: 10.1021/ct500090q.
Miao, Y., Sinko, W., Pierce, L., Bucher, D., Walker, R. C., & McCammon, J. A. (2014). Improved Reweighting of Accelerated Molecular Dynamics Simulations for Free Energy Calculation. Journal of chemical theory and computation, 10(7), 2677-2689. https://doi.org/10.1021/ct500090q
Miao, Yinglong, et al. "Improved Reweighting of Accelerated Molecular Dynamics Simulations for Free Energy Calculation." Journal of chemical theory and computation vol. 10,7 (2014): 2677-2689. doi: https://doi.org/10.1021/ct500090q
Miao Y, Sinko W, Pierce L, Bucher D, Walker RC, McCammon JA. Improved Reweighting of Accelerated Molecular Dynamics Simulations for Free Energy Calculation. J Chem Theory Comput. 2014 Jul 08;10(7):2677-2689. doi: 10.1021/ct500090q. Epub 2014 May 01. PMID: 25061441; PMCID: PMC4095935.
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Optimizing the Poisson Dielectric Boundary with Explicit Solvent Forces and Energies:  Lessons Learned with Atom-Centered Dielectric Functions.

Journal of chemical theory and computation

Swanson JM, Wagoner JA, Baker NA, McCammon JA.
PMID: 26627162
J Chem Theory Comput. 2007 Jan;3(1):170-83. doi: 10.1021/ct600216k.

Accurate implicit solvent models require parameters that have been optimized in a system- or atom-specific manner on the basis of experimental data or more rigorous explicit solvent simulations. Models based on the Poisson or Poisson-Boltzmann equation are particularly sensitive...

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Swanson JM, Wagoner JA, Baker NA, et al. Optimizing the Poisson Dielectric Boundary with Explicit Solvent Forces and Energies:  Lessons Learned with Atom-Centered Dielectric Functions. J Chem Theory Comput. 2007;3(1):170-83doi: 10.1021/ct600216k.
Swanson, J. M., Wagoner, J. A., Baker, N. A., & McCammon, J. A. (2007). Optimizing the Poisson Dielectric Boundary with Explicit Solvent Forces and Energies:  Lessons Learned with Atom-Centered Dielectric Functions. Journal of chemical theory and computation, 3(1), 170-83. https://doi.org/10.1021/ct600216k
Swanson, Jessica M J, et al. "Optimizing the Poisson Dielectric Boundary with Explicit Solvent Forces and Energies:  Lessons Learned with Atom-Centered Dielectric Functions." Journal of chemical theory and computation vol. 3,1 (2007): 170-83. doi: https://doi.org/10.1021/ct600216k
Swanson JM, Wagoner JA, Baker NA, McCammon JA. Optimizing the Poisson Dielectric Boundary with Explicit Solvent Forces and Energies:  Lessons Learned with Atom-Centered Dielectric Functions. J Chem Theory Comput. 2007 Jan;3(1):170-83. doi: 10.1021/ct600216k. PMID: 26627162.
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Iron isotope fractionation and the oxygen fugacity of the mantle.

Science (New York, N.Y.)

Williams HM, McCammon CA, Peslier AH, Halliday AN, Teutsch N, Levasseur S, Burg JP.
PMID: 15192225
Science. 2004 Jun 11;304(5677):1656-9. doi: 10.1126/science.1095679.

The oxygen fugacity of the mantle exerts a fundamental influence on mantle melting, volatile speciation, and the development of the atmosphere. However, its evolution through time is poorly understood. Changes in mantle oxidation state should be reflected in the...

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Williams HM, McCammon CA, Peslier AH, et al. Iron isotope fractionation and the oxygen fugacity of the mantle. Science. 2004;304(5677):1656-9doi: 10.1126/science.1095679.
Williams, H. M., McCammon, C. A., Peslier, A. H., Halliday, A. N., Teutsch, N., Levasseur, S., & Burg, J. P. (2004). Iron isotope fractionation and the oxygen fugacity of the mantle. Science (New York, N.Y.), 304(5677), 1656-9. https://doi.org/10.1126/science.1095679
Williams, Helen M, et al. "Iron isotope fractionation and the oxygen fugacity of the mantle." Science (New York, N.Y.) vol. 304,5677 (2004): 1656-9. doi: https://doi.org/10.1126/science.1095679
Williams HM, McCammon CA, Peslier AH, Halliday AN, Teutsch N, Levasseur S, Burg JP. Iron isotope fractionation and the oxygen fugacity of the mantle. Science. 2004 Jun 11;304(5677):1656-9. doi: 10.1126/science.1095679. PMID: 15192225.
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AFMPB: An Adaptive Fast Multipole Poisson-Boltzmann Solver for Calculating Electrostatics in Biomolecular Systems.

Computer physics communications

Lu B, Cheng X, Huang J, McCammon JA.
PMID: 20532187
Comput Phys Commun. 2010 Jun 01;181(6):1150-1160. doi: 10.1016/j.cpc.2010.02.015.

A Fortran program package is introduced for rapid evaluation of the electrostatic potentials and forces in biomolecular systems modeled by the linearized Poisson-Boltzmann equation. The numerical solver utilizes a well-conditioned boundary integral equation (BIE) formulation, a node-patch discretization scheme,...

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Lu B, Cheng X, Huang J, et al. AFMPB: An Adaptive Fast Multipole Poisson-Boltzmann Solver for Calculating Electrostatics in Biomolecular Systems. Comput Phys Commun. 2010;181(6):1150-1160doi: 10.1016/j.cpc.2010.02.015.
Lu, B., Cheng, X., Huang, J., & McCammon, J. A. (2010). AFMPB: An Adaptive Fast Multipole Poisson-Boltzmann Solver for Calculating Electrostatics in Biomolecular Systems. Computer physics communications, 181(6), 1150-1160. https://doi.org/10.1016/j.cpc.2010.02.015
Lu, Benzhuo, et al. "AFMPB: An Adaptive Fast Multipole Poisson-Boltzmann Solver for Calculating Electrostatics in Biomolecular Systems." Computer physics communications vol. 181,6 (2010): 1150-1160. doi: https://doi.org/10.1016/j.cpc.2010.02.015
Lu B, Cheng X, Huang J, McCammon JA. AFMPB: An Adaptive Fast Multipole Poisson-Boltzmann Solver for Calculating Electrostatics in Biomolecular Systems. Comput Phys Commun. 2010 Jun 01;181(6):1150-1160. doi: 10.1016/j.cpc.2010.02.015. PMID: 20532187; PMCID: PMC2880819.
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Browndye: A Software Package for Brownian Dynamics.

Computer physics communications

Huber GA, McCammon JA.
PMID: 21132109
Comput Phys Commun. 2010 Nov 01;181(11):1896-1905. doi: 10.1016/j.cpc.2010.07.022.

A new software package, Browndye, is presented for simulating the diffusional encounter of two large biological molecules. It can be used to estimate second-order rate constants and encounter probabilities, and to explore reaction trajectories. Browndye builds upon previous knowledge...

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Huber GA, McCammon JA. Browndye: A Software Package for Brownian Dynamics. Comput Phys Commun. 2010;181(11):1896-1905doi: 10.1016/j.cpc.2010.07.022.
Huber, G. A., & McCammon, J. A. (2010). Browndye: A Software Package for Brownian Dynamics. Computer physics communications, 181(11), 1896-1905. https://doi.org/10.1016/j.cpc.2010.07.022
Huber, Gary A, and McCammon, J Andrew. "Browndye: A Software Package for Brownian Dynamics." Computer physics communications vol. 181,11 (2010): 1896-1905. doi: https://doi.org/10.1016/j.cpc.2010.07.022
Huber GA, McCammon JA. Browndye: A Software Package for Brownian Dynamics. Comput Phys Commun. 2010 Nov 01;181(11):1896-1905. doi: 10.1016/j.cpc.2010.07.022. PMID: 21132109; PMCID: PMC2994412.
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"New-version-fast-multipole-method" accelerated electrostatic interactions in biomolecular systems.

Journal of computational physics

Lu B, Cheng X, McCammon JA.
PMID: 18379638
J Comput Phys. 2007 Oct 01;226(2):1348-1366. doi: 10.1016/j.jcp.2007.05.026.

In this paper, we present an efficient and accurate numerical algorithm for calculating the electrostatic interactions in biomolecular systems. In our scheme, a boundary integral equation (BIE) approach is applied to discretize the linearized Poisson-Boltzmann (PB) equation. The resulting...

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Lu B, Cheng X, McCammon JA. "New-version-fast-multipole-method" accelerated electrostatic interactions in biomolecular systems. J Comput Phys. 2007;226(2):1348-1366doi: 10.1016/j.jcp.2007.05.026.
Lu, B., Cheng, X., & McCammon, J. A. (2007). "New-version-fast-multipole-method" accelerated electrostatic interactions in biomolecular systems. Journal of computational physics, 226(2), 1348-1366. https://doi.org/10.1016/j.jcp.2007.05.026
Lu, Benzhuo, et al. ""New-version-fast-multipole-method" accelerated electrostatic interactions in biomolecular systems." Journal of computational physics vol. 226,2 (2007): 1348-1366. doi: https://doi.org/10.1016/j.jcp.2007.05.026
Lu B, Cheng X, McCammon JA. "New-version-fast-multipole-method" accelerated electrostatic interactions in biomolecular systems. J Comput Phys. 2007 Oct 01;226(2):1348-1366. doi: 10.1016/j.jcp.2007.05.026. PMID: 18379638; PMCID: PMC2084081.
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Showing 1 to 12 of 168 entries