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Jeffery B. Klauda, Ph.D. - Publications

Affiliations: 
University of Delaware, Newark, DE, United States 
Area:
Statistical, Quantum, and Experimental Thermodynamics
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52 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2016 Zhuang X, Dávila-Contreras EM, Beaven AH, Im W, Klauda JB. An extensive simulation study of lipid bilayer properties with different head groups, acyl chain lengths, and chain saturations. Biochimica Et Biophysica Acta. PMID 27664502 DOI: 10.1016/J.Bbamem.2016.09.016  1
2016 Zhuang X, Klauda JB. Modeling structural transitions from the periplasmic-open state of lactose permease and interpretations of spin label experiments. Biochimica Et Biophysica Acta. PMID 27107553 DOI: 10.1016/J.Bbamem.2016.04.008  1
2015 MacDermaid CM, Kashyap HK, DeVane RH, Shinoda W, Klauda JB, Klein ML, Fiorin G. Molecular dynamics simulations of cholesterol-rich membranes using a coarse-grained force field for cyclic alkanes. The Journal of Chemical Physics. 143: 243144. PMID 26723629 DOI: 10.1063/1.4937153  1
2015 Lee J, Cheng X, Swails JM, Yeom MS, Eastman PK, Lemkul JA, Wei S, Buckner J, Jeong JC, Qi Y, Jo S, Pande VS, Case DA, Brooks CL, MacKerell AD, ... Klauda JB, et al. CHARMM-GUI Input Generator for NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM Simulations Using the CHARMM36 Additive Force Field. Journal of Chemical Theory and Computation. PMID 26631602 DOI: 10.1021/Acs.Jctc.5B00935  1
2015 Choudhary R, Klauda JB. Title: The Simultaneous Mass and Energy Evaporation (SM2E) Model. Journal of Occupational and Environmental Hygiene. 1-41. PMID 26595699 DOI: 10.1080/15459624.2015.1101123  1
2015 Wu EL, Qi Y, Park S, Mallajosyula SS, MacKerell AD, Klauda JB, Im W. Insight into Early-Stage Unfolding of GPI-Anchored Human Prion Protein. Biophysical Journal. 109: 2090-2100. PMID 26588568 DOI: 10.1016/J.Bpj.2015.10.009  1
2015 Qi Y, Cheng X, Lee J, Vermaas JV, Pogorelov TV, Tajkhorshid E, Park S, Klauda JB, Im W. CHARMM-GUI HMMM Builder for Membrane Simulations with the Highly Mobile Membrane-Mimetic Model. Biophysical Journal. 109: 2012-2022. PMID 26588561 DOI: 10.1016/J.Bpj.2015.10.008  1
2015 Park S, Beaven AH, Klauda JB, Im W. How Tolerant are Membrane Simulations with Mismatch in Area per Lipid between Leaflets? Journal of Chemical Theory and Computation. 11: 3466-3477. PMID 26575780 DOI: 10.1021/Acs.Jctc.5B00232  1
2015 Jo S, Wu EL, Stuhlsatz D, Klauda JB, MacKerell AD, Widmalm G, Im W. Lipopolysaccharide membrane building and simulation. Methods in Molecular Biology (Clifton, N.J.). 1273: 391-406. PMID 25753722 DOI: 10.1007/978-1-4939-2343-4_24  1
2014 Kern NR, Lee HS, Wu EL, Park S, Vanommeslaeghe K, MacKerell AD, Klauda JB, Jo S, Im W. Lipid-linked oligosaccharides in membranes sample conformations that facilitate binding to oligosaccharyltransferase. Biophysical Journal. 107: 1885-95. PMID 25418169 DOI: 10.1016/J.Bpj.2014.09.007  1
2014 Wu EL, Cheng X, Jo S, Rui H, Song KC, Dávila-Contreras EM, Qi Y, Lee J, Monje-Galvan V, Venable RM, Klauda JB, Im W. CHARMM-GUI Membrane Builder toward realistic biological membrane simulations. Journal of Computational Chemistry. 35: 1997-2004. PMID 25130509 DOI: 10.1002/Jcc.23702  1
2014 Venable RM, Sodt AJ, Rogaski B, Rui H, Hatcher E, MacKerell AD, Pastor RW, Klauda JB. CHARMM all-atom additive force field for sphingomyelin: elucidation of hydrogen bonding and of positive curvature. Biophysical Journal. 107: 134-45. PMID 24988348 DOI: 10.1016/J.Bpj.2014.05.034  1
2014 Zhuang X, Makover JR, Im W, Klauda JB. A systematic molecular dynamics simulation study of temperature dependent bilayer structural properties. Biochimica Et Biophysica Acta. 1838: 2520-9. PMID 24953542 DOI: 10.1016/J.Bbamem.2014.06.010  1
2014 Wu EL, Fleming PJ, Yeom MS, Widmalm G, Klauda JB, Fleming KG, Im W. E. coli outer membrane and interactions with OmpLA. Biophysical Journal. 106: 2493-502. PMID 24896129 DOI: 10.1016/J.Bpj.2014.04.024  1
2014 Subramanian D, Klauda JB, Collings PJ, Anisimov MA. Mesoscale phenomena in ternary solutions of tertiary butyl alcohol, water, and propylene oxide. The Journal of Physical Chemistry. B. 118: 5994-6006. PMID 24823321 DOI: 10.1021/Jp4125183  1
2014 Wu EL, Qi Y, Song KC, Klauda JB, Im W. Preferred orientations of phosphoinositides in bilayers and their implications in protein recognition mechanisms. The Journal of Physical Chemistry. B. 118: 4315-25. PMID 24689790 DOI: 10.1021/Jp500610T  1
2014 Jeong JC, Jo S, Wu EL, Qi Y, Monje-Galvan V, Yeom MS, Gorenstein L, Chen F, Klauda JB, Im W. ST-analyzer: a web-based user interface for simulation trajectory analysis. Journal of Computational Chemistry. 35: 957-63. PMID 24638223 DOI: 10.1002/Jcc.23584  1
2013 Subramanian D, Boughter CT, Klauda JB, Hammouda B, Anisimov MA. Mesoscale inhomogeneities in aqueous solutions of small amphiphilic molecules Faraday Discussions. 167: 217-238. PMID 24640493 DOI: 10.1039/C3Fd00070B  1
2013 Villanueva DY, Lim JB, Klauda JB. Influence of ester-modified lipids on bilayer structure. Langmuir : the Acs Journal of Surfaces and Colloids. 29: 14196-203. PMID 24156542 DOI: 10.1021/La403919H  1
2013 Wu EL, Engström O, Jo S, Stuhlsatz D, Yeom MS, Klauda JB, Widmalm G, Im W. Molecular dynamics and NMR spectroscopy studies of E. coli lipopolysaccharide structure and dynamics. Biophysical Journal. 105: 1444-55. PMID 24047996 DOI: 10.1016/J.Bpj.2013.08.002  1
2013 Cheng X, Jo S, Lee HS, Klauda JB, Im W. CHARMM-GUI micelle builder for pure/mixed micelle and protein/micelle complex systems. Journal of Chemical Information and Modeling. 53: 2171-80. PMID 23865552 DOI: 10.1021/Ci4002684  1
2012 Klauda JB, Monje V, Kim T, Im W. Improving the CHARMM force field for polyunsaturated fatty acid chains. The Journal of Physical Chemistry. B. 116: 9424-31. PMID 22697583 DOI: 10.1021/Jp304056P  1
2012 Kwon T, Roux B, Jo S, Klauda JB, Harris AL, Bargiello TA. Molecular dynamics simulations of the Cx26 hemichannel: insights into voltage-dependent loop-gating. Biophysical Journal. 102: 1341-51. PMID 22455917 DOI: 10.1016/J.Bpj.2012.02.009  1
2011 Song KC, Livanec PW, Klauda JB, Kuczera K, Dunn RC, Im W. Orientation of fluorescent lipid analogue BODIPY-PC to probe lipid membrane properties: insights from molecular dynamics simulations. The Journal of Physical Chemistry. B. 115: 6157-65. PMID 21513278 DOI: 10.1021/Jp109629V  1
2010 Jo S, Rui H, Lim JB, Klauda JB, Im W. Cholesterol flip-flop: insights from free energy simulation studies. The Journal of Physical Chemistry. B. 114: 13342-8. PMID 20923227 DOI: 10.1021/Jp108166K  1
2010 Pendse PY, Brooks BR, Klauda JB. Probing the periplasmic-open state of lactose permease in response to sugar binding and proton translocation. Journal of Molecular Biology. 404: 506-21. PMID 20875429 DOI: 10.1016/J.Jmb.2010.09.045  1
2010 Klauda JB, Venable RM, Freites JA, O'Connor JW, Tobias DJ, Mondragon-Ramirez C, Vorobyov I, MacKerell AD, Pastor RW. Update of the CHARMM all-atom additive force field for lipids: validation on six lipid types. The Journal of Physical Chemistry. B. 114: 7830-43. PMID 20496934 DOI: 10.1021/Jp101759Q  1
2009 Jo S, Lim JB, Klauda JB, Im W. CHARMM-GUI Membrane Builder for mixed bilayers and its application to yeast membranes. Biophysical Journal. 97: 50-8. PMID 19580743 DOI: 10.1016/J.Bpj.2009.04.013  1
2009 Singh RP, Brooks BR, Klauda JB. Binding and release of cholesterol in the Osh4 protein of yeast. Proteins. 75: 468-77. PMID 18937371 DOI: 10.1002/Prot.22263  1
2008 Miller BT, Singh RP, Klauda JB, Hodoscek M, Brooks BR, Woodcock HL. CHARMMing: a new, flexible web portal for CHARMM. Journal of Chemical Information and Modeling. 48: 1920-9. PMID 18698840 DOI: 10.1021/Ci800133B  1
2008 Klauda JB, Eldho NV, Gawrisch K, Brooks BR, Pastor RW. Collective and noncollective models of NMR relaxation in lipid vesicles and multilayers. The Journal of Physical Chemistry. B. 112: 5924-9. PMID 18179193 DOI: 10.1021/Jp075641W  1
2008 Klauda JB, Brooks BR. CHARMM force field parameters for nitroalkanes and nitroarenes Journal of Chemical Theory and Computation. 4: 107-115. DOI: 10.1021/ct700191v  1
2008 Klauda JB, Venable RM, MacKerell AD, Pastor RW. Chapter 1 Considerations for Lipid Force Field Development Current Topics in Membranes. 60: 1-48. DOI: 10.1016/S1063-5823(08)00001-X  1
2007 Klauda JB, Wu X, Pastor RW, Brooks BR. Long-range Lennard-Jones and electrostatic interactions in interfaces: application of the isotropic periodic sum method. The Journal of Physical Chemistry. B. 111: 4393-400. PMID 17425357 DOI: 10.1021/Jp068767M  1
2007 Klauda JB, Brooks BR. Sugar binding in lactose permease: anomeric state of a disaccharide influences binding structure. Journal of Molecular Biology. 367: 1523-34. PMID 17320103 DOI: 10.1016/J.Jmb.2007.02.001  1
2006 Klauda JB, Brooks BR, Pastor RW. Dynamical motions of lipids and a finite size effect in simulations of bilayers. The Journal of Chemical Physics. 125: 144710. PMID 17042634 DOI: 10.1063/1.2354486  1
2006 Klauda JB, Kucerka N, Brooks BR, Pastor RW, Nagle JF. Simulation-based methods for interpreting x-ray data from lipid bilayers. Biophysical Journal. 90: 2796-807. PMID 16443652 DOI: 10.1529/Biophysj.105.075697  1
2005 Klauda JB, Brooks BR, MacKerell AD, Venable RM, Pastor RW. An ab initio study on the torsional surface of alkanes and its effect on molecular simulations of alkanes and a DPPC bilayer. The Journal of Physical Chemistry. B. 109: 5300-11. PMID 16863197 DOI: 10.1021/Jp0468096  1
2005 Arora G, Klauda JB, Sandler SI. A comparative study of nitrogen physisorption on different C 70 crystal structures using an ab initio based potential Journal of Physical Chemistry B. 109: 17267-17273. PMID 16853204 DOI: 10.1021/Jp050590T  1
2005 Klauda JB, Pastor RW, Brooks BR. Adjacent gauche stabilization in linear alkanes: implications for polymer models and conformational analysis. The Journal of Physical Chemistry. B. 109: 15684-6. PMID 16852989 DOI: 10.1021/Jp0527608  1
2005 Jiang J, Klauda JB, Sandler SI. Hierarchical modeling N2 adsorption on the surface of and within a C60 crystal: from quantum mechanics to molecular simulation. The Journal of Physical Chemistry. B. 109: 4731-7. PMID 16851555 DOI: 10.1021/Jp0479567  1
2005 Klauda JB, Sandler SI. Global distribution of methane hydrate in ocean sediment Energy and Fuels. 19: 459-470. DOI: 10.1021/Ef049798O  1
2005 Klauda JB, Brooks BR, Pastor RW. Structure and dynamics of lipid membranes: How can simulations aid experiments? Aiche Annual Meeting, Conference Proceedings. 10460.  1
2005 Klauda JB, Wu X, Pastor RW, Brooks BR. Importance of including long-range interactions in simulations of biologically relevant 2d surfaces Aiche Annual Meeting, Conference Proceedings. 10436.  1
2004 Klauda JB, Jiang J, Sandler SI. An ab initio study on the effect of carbon surface curvature and ring structure on N2(O2) - Carbon intermodular potentials Journal of Physical Chemistry B. 108: 9842-9851. DOI: 10.1021/Jp037897H  1
2004 Klauda JB, Garrison SL, Jiang J, Arora G, Sandler SI. HM-IE: Quantum chemical hybrid methods for calculating interaction energies Journal of Physical Chemistry A. 108: 107-112. DOI: 10.1021/Jp035639E  1
2003 Jiang JW, Klauda JB, Sandler SI. Monte Carlo simulation of O2 and N2 adsorption in nanoporous carbon (C168 Schwarzite) Langmuir. 19: 3512-3518. DOI: 10.1021/La020319S  1
2003 Klauda JB, Sandler SI. Predictions of gas hydrate phase equilibria and amounts in natural sediment porous media Marine and Petroleum Geology. 20: 459-470. DOI: 10.1016/S0264-8172(03)00064-3  1
2003 Klauda JB, Sandler SI. Phase behavior of clathrate hydrates: A model for single and multiple gas component hydrates Chemical Engineering Science. 58: 27-41. DOI: 10.1016/S0009-2509(02)00435-9  1
2002 Klauda JB, Sandler SI. Ab initio intermolecular potentials for gas hydrates and their predictions Journal of Physical Chemistry B. 106: 5722-5732. DOI: 10.1021/Jp0135914  1
2001 Klauda JB, Sandler SI. Modeling gas hydrate phase equilibria in laboratory and natural porous media Industrial and Engineering Chemistry Research. 40: 4197-4208. DOI: 10.1021/Ie000961M  1
2000 Klauda JB, Sandler SI. A fugacity model for gas hydrate phase equilibria Industrial and Engineering Chemistry Research. 39: 3377-3386. DOI: 10.1021/Ie000322B  1
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