robertvacha's library 149 articles Export

	Elucidating the Mechanism of Lipid Membrane-Induced IAPP Fibrillogenesis and Its Inhibition by the Red Wine Compound Resveratrol: A Synchrotron X-ray Reflectivity Study [My Copy] Journal of the American Chemical Society, Vol. 131, No. 27. (15 July 2009), pp. 9516-9521. by Florian Evers, Christoph Jeworrek, Sebastian Tiemeyer, et al.Katrin Weise, Daniel Sellin, Michael Paulus, Bernd Struth, Metin Tolan, Roland Winter posted to membrane by robertvacha on 2009-07-10 11:31:20 as
	GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation [My Copy] Journal of Chemical Theory and Computation, Vol. 4, No. 3. (1 March 2008), pp. 435-447. by Berk Hess, Carsten Kutzner, David van der Spoel, Erik Lindahl posted to no-tag by robertvacha on 2009-06-26 10:57:33 as along with 23 people and 2 groups sunnytov softsimu parnell rabio oteri krapnik rodrigofaccioli pavanghatty janneb ZhangYinhe okapi flbarroso marceavi A_Coletta_Thesis choonpeng Lombardo_7 jwm daevans mmuecke sobolevnrm r2s2 middledomain loison Structural Biology Group TorVergata baker-group
	Ions at Aqueous Interfaces: From Water Surface to Hydrated Proteins [My Copy] Annual Review of Physical Chemistry, Vol. 59, No. 1. (2008), pp. 343-366. by Pavel Jungwirth, Bernd Winter posted to airwater ions by robertvacha on 2009-04-06 08:39:43 as along with 2 people r3vi flbarroso
	Electrical charges arising at a liquid-gas interface [My Copy] Proceedings of the Physical Society of London, Vol. 37, No. 1. (1924), pp. 195-214. by H. W. Gilbert, P. E. Shaw posted to h3o oh- by robertvacha on 2009-03-27 13:09:25 as
	Effect of Ions on a Dipalmitoyl Phosphatidylcholine Bilayer. A Molecular Dynamics Simulation Study [My Copy] J. Phys. Chem. B (15 January 2008) by A. Cordomi, O. Edholm, J. J. Perez posted to membrane-ions by robertvacha on 2008-09-21 16:14:14 as along with 4 people and 1 group arnaucordomi sobolevnrm softsimu dimka baker-group
	Many-body effects in molecular dynamics simulations of Na[sup + ](H[sub 2]O)[sub n] and Cl[sup - ](H[sub 2]O)[sub n] clusters [My Copy] The Journal of Chemical Physics, Vol. 95, No. 3. (1991), pp. 1954-1963. by Lalith Perera, Max L. Berkowitz posted to airwater by robertvacha on 2008-09-21 15:42:49 as
	Molecular dynamics simulations of asymmetric NaCl and KCl solutions separated by phosphatidylcholine bilayers: potential drops and structural changes induced by strong Na+-lipid interactions and finite size effects [My Copy] Biophys. J. (25 January 2008), biophysj.107.116335. by Sun-Joo Lee, Yuhua Song, Nathan A. Baker posted to membrane-ions by robertvacha on 2008-09-21 15:38:53 as along with 4 people and 1 group sunhwan sunnytov sobolevnrm paulschlesinger baker-group
	Diffuse scattering provides material parameters and electron density profiles of biomembranes [My Copy] Physical Review E, Vol. 69, No. 4. (30 April 2004), 040901. by Yufeng Liu, John F. Nagle posted to membrane by robertvacha on 2008-09-21 15:29:48 as along with 1 person softsimu
	Parameters of monovalent ions in the AMBER-99 forcefield: assessment of inaccuracies and proposed improvements. [My Copy] The journal of physical chemistry. B, Vol. 111, No. 41. (18 October 2007), pp. 11884-11887. by Alan A. Chen, Rohit V. Pappu posted to ion-pairing ions by robertvacha on 2008-09-21 15:27:52 as along with 2 people and 1 group sobolevnrm middledomain baker-group
	Spontaneous Formation of KCl Aggregates in Biomolecular Simulations: A Force Field Issue? [My Copy] J. Chem. Theory Comput., Vol. 3, No. 5. (11 September 2007), pp. 1851-1859. by P. Auffinger, T. E. Cheatham, A. C. Vaiana posted to ion-pairing ions by robertvacha on 2008-09-21 15:24:51 as along with 1 person softsimu
	Particle mesh Ewald: An N [center-dot] log(N) method for Ewald sums in large systems [My Copy] The Journal of Chemical Physics, Vol. 98, No. 12. (1993), pp. 10089-10092. by Tom Darden, Darrin York, Lee Pedersen posted to gromacs by robertvacha on 2008-09-21 15:11:26 as along with 12 people sunnytov bmduggan rpetrenko r2s2 A_Coletta_Thesis mleis and_ped10 allmensch easybakemuffin RamuAnandakrishnan tji ashaytan
	Biomolecular simulations of membranes: Physical properties from different force fields [My Copy] The Journal of Chemical Physics, Vol. 128, No. 12. (2008) by Shirley W. I. Siu, Robert Vácha, Pavel Jungwirth, Rainer A. Böckmann posted to membrane-ions by robertvacha on 2008-09-21 15:03:55 as along with 4 people and 1 group krapnik sobolevnrm paulschlesinger sunhwan baker-group
	Free-energy analysis of solubilization in micelle [My Copy] The Journal of Chemical Physics, Vol. 124, No. 15. (2006) by Nobuyuki Matubayasi, Kuo K. Liang, Masaru Nakahara posted to energy free by robertvacha on 2008-09-09 12:03:12 as
	Chemical equilibrium of formaldehyde and methanediol in hot water: Free-energy analysis of the solvent effect [My Copy] Journal of Molecular Liquids In EMLG/JMLG 2005 Special Issue, Annual Meeting of the EMLG/JMLG 2005, Vol. 134, No. 1-3. (15 May 2007), pp. 58-63. by Nobuyuki Matubayasi, Saiko Morooka, Masaru Nakahara, Hideaki Takahashi posted to energy free by robertvacha on 2008-09-09 12:02:17 as
	An approach to the solvation free energy in terms of the distribution functions of the solute-solvent interaction energy [My Copy] Journal of Molecular Liquids In Oktaki Symposium of the Association of Japanese Solution Chemists, Ritsumeikan University, Kusatsu, Shiga, Vol. 119, No. 1-3. (15 May 2005), pp. 23-29. by Nobuyuki Matubayasi, Masaru Nakahara posted to no-tag by robertvacha on 2008-09-09 12:01:16 as
	A novel quantum mechanical/molecular mechanical approach to the free energy calculation for isomerization of glycine in aqueous solution [My Copy] The Journal of Chemical Physics, Vol. 123, No. 12. (2005) by Hideaki Takahashi, Yuko Kawashima, Tomoshige Nitta, Nobuyuki Matubayasi posted to energy free by robertvacha on 2008-09-05 15:07:50 as
	Theory of solutions in the energy representation. III. Treatment of the molecular flexibility [My Copy] The Journal of Chemical Physics, Vol. 119, No. 18. (2003), pp. 9686-9702. by Nobuyuki Matubayasi, Masaru Nakahara posted to energy free by robertvacha on 2008-09-05 14:57:13 as
	Theory of solutions in the energy representation. II. Functional for the chemical potential [My Copy] The Journal of Chemical Physics, Vol. 117, No. 8. (2002), pp. 3605-3616. by Nobuyuki Matubayasi, Masaru Nakahara posted to energy free by robertvacha on 2008-09-05 14:56:39 as
	Theory of solutions in the energetic representation. I. Formulation [My Copy] The Journal of Chemical Physics, Vol. 113, No. 15. (2000), pp. 6070-6081. by Nobuyuki Matubayasi, Masaru Nakahara posted to energy free by robertvacha on 2008-09-05 14:56:00 as along with 1 person mikaellund
	Permeation Process of Small Molecules across Lipid Membranes Studied by Molecular Dynamics Simulations [My Copy] J. Phys. Chem., Vol. 100, No. 41. (10 October 1996), pp. 16729-16738. by S. J. Marrink, H. J. C. Berendsen posted to membrane by robertvacha on 2008-07-24 08:25:27 as along with 2 people andreasauerwein ashaytan
	Article DOI Lookup [My Copy] posted to membrane water by robertvacha on 2008-07-24 08:24:04 as
	Atomistic simulations of biologically realistic transmembrane potential gradients [My Copy] The Journal of Chemical Physics, Vol. 121, No. 22. (2004), pp. 10847-10851. by Jonathan N. Sachs, Paul S. Crozier, Thomas B. Woolf posted to asymmetry membrane by robertvacha on 2008-06-25 07:47:18 as along with 1 person sunnytov
	Phospholipid composition of the mammalian red cell membrane can be rationalized by a superlattice model [My Copy] Proceedings of the National Academy of Sciences, Vol. 95, No. 9. (28 April 1998), pp. 4964-4969. by J. A. Virtanen, K. H. Cheng, P. Somerharju posted to membrane by robertvacha on 2008-06-20 19:36:32 as along with 1 person ferin
	Molecular dynamics simulation of dipalmitoylphosphatidylserine bilayer with Na+ counterions. [My Copy] Biophysical journal, Vol. 82, No. 4. (April 2002), pp. 1818-1827. by S. A. Pandit, M. L. Berkowitz posted to membrane membrane-ions by robertvacha on 2008-06-20 19:20:05 as
	An algorithm to describe molecular scale rugged surfaces and its application to the study of a water/lipid bilayer interface [My Copy] The Journal of Chemical Physics, Vol. 119, No. 4. (2003), pp. 2199-2205. by Sagar A. Pandit, David Bostick, Max L. Berkowitz posted to membrane by robertvacha on 2008-06-20 19:19:45 as
	Mixed Bilayer Containing Dipalmitoylphosphatidylcholine and Dipalmitoylphosphatidylserine: Lipid Complexation, Ion Binding, and Electrostatics [My Copy] Biophys. J., Vol. 85, No. 5. (1 November 2003), pp. 3120-3131. by Sagar A. Pandit, David Bostick, Max L. Berkowitz posted to membrane membrane-ions by robertvacha on 2008-06-20 19:19:03 as along with 1 person softsimu
	Complexation of phosphatidylcholine lipids with cholesterol. [My Copy] Biophysical journal, Vol. 86, No. 3. (March 2004), pp. 1345-1356. by S. A. Pandit, D. Bostick, M. L. Berkowitz posted to membrane by robertvacha on 2008-06-20 19:18:27 as along with 1 person paulschlesinger
	Molecular dynamics study of charged dendrimers in salt-free solution: Effect of counterions [My Copy] The Journal of Chemical Physics, Vol. 124, No. 9. (2006) by Andrey A. Gurtovenko, Sergey V. Lyulin, Mikko Karttunen, Ilpo Vattulainen posted to membrane by robertvacha on 2008-06-20 19:13:31 as along with 1 person softsimu
	Molecular dynamics study of charged dendrimers in salt-free solution: effect of counterions. [My Copy] The Journal of chemical physics, Vol. 124, No. 9. (7 March 2006) by A. A. Gurtovenko, S. V. Lyulin, M. Karttunen, I. Vattulainen posted to membrane by robertvacha on 2008-06-20 19:13:07 as
	Atomic-Scale Structure and Electrostatics of Anionic Palmitoyloleoylphosphatidylglycerol Lipid Bilayers with Na+ Counterions [My Copy] Biophysical Journal, Vol. 92, No. 4. (15 February 2007), pp. 1114-1124. by W. Zhao, T. Rog, A. Gurtovenko, I. Vattulainen, M. Karttunen posted to membrane membrane-ions by robertvacha on 2008-06-20 19:11:36 as along with 2 people flbarroso softsimu
	Molecular Mechanism for Lipid Flip-Flops [My Copy] J. Phys. Chem. B, Vol. 111, No. 48. (6 December 2007), pp. 13554-13559. by A. A. Gurtovenko, I. Vattulainen posted to asymmetry membrane by robertvacha on 2008-06-20 19:10:24 as along with 2 people and 1 group softsimu sobolevnrm baker-group
	Molecular dynamics simulation of a dipalmitoylphosphatidylcholine bilayer with NaCl. [My Copy] Biophysical journal, Vol. 84, No. 6. (1 June 2003), pp. 3743-3750. by Sagar A. Pandit, David Bostick, Max L. Berkowitz posted to membrane-ions by robertvacha on 2008-06-20 19:01:03 as along with 2 people dimka softsimu
	Aqueous solutions next to phospholipid membrane surfaces: Insights from simulations [My Copy] Chem. Rev., Vol. 106, No. 4. (2006), pp. 1527-1539. by M. L. Berkowitz, D. L. Bostick, S. Pandit posted to membrane membrane-ions by robertvacha on 2008-06-20 19:00:39 as along with 1 person softsimu
	Effect of sodium chloride on a lipid bilayer. [My Copy] Biophysical journal, Vol. 85, No. 3. (September 2003), pp. 1647-1655. by R. A. Böckmann, A. Hac, T. Heimburg, H. Grubmüller posted to membrane-ions by robertvacha on 2008-06-20 18:59:09 as along with 1 person sunnytov
	Molecular simulation analysis and X-ray absorption measurement of Ca2+, K+ and Cl- ions in solution. [My Copy] The journal of physical chemistry. B, Vol. 110, No. 47. (30 November 2006), pp. 23644-23654. by L. X. Dang, G. K. Schenter, V. A. Glezakou, J. L. Fulton posted to md by robertvacha on 2008-06-20 18:58:22 as
	Cationic DMPC/DMTAP Lipid Bilayers: Molecular Dynamics Study [My Copy] Biophys. J., Vol. 86, No. 6. (1 June 2004), pp. 3461-3472. by Andrey A. Gurtovenko, Michael Patra, Mikko Karttunen, Ilpo Vattulainen posted to membrane by robertvacha on 2008-06-20 18:56:47 as along with 2 people sunhwan softsimu
	Effect of Monovalent Salt on Cationic Lipid Membranes As Revealed by Molecular Dynamics Simulations [My Copy] J. Phys. Chem. B, Vol. 109, No. 44. (10 November 2005), pp. 21126-21134. by A. A. Gurtovenko, M. Miettinen, M. Karttunen, I. Vattulainen posted to membrane-ions by robertvacha on 2008-06-20 18:56:23 as along with 1 person softsimu
	Pore formation coupled to ion transport through lipid membranes as induced by transmembrane ionic charge imbalance: atomistic molecular dynamics study. [My Copy] J Am Chem Soc, Vol. 127, No. 50. (21 December 2005), pp. 17570-17571. by A. A. Gurtovenko, I. Vattulainen posted to membrane-ions by robertvacha on 2008-06-20 18:56:09 as along with 1 person divadyrral
	Ion Leakage through Transient Water Pores in Protein-Free Lipid Membranes Driven by Transmembrane Ionic Charge Imbalance [My Copy] Biophys. J., Vol. 92, No. 6. (15 March 2007), pp. 1878-1890. by Andrey A. Gurtovenko, Ilpo Vattulainen posted to membrane-ions by robertvacha on 2008-06-20 18:55:36 as along with 1 person softsimu
	Lipid transmembrane asymmetry and intrinsic membrane potential: two sides of the same coin. [My Copy] Journal of the American Chemical Society, Vol. 129, No. 17. (2 May 2007), pp. 5358-5359. by A. A. Gurtovenko, I. Vattulainen posted to membrane by robertvacha on 2008-06-20 18:55:17 as
	Structure and Dynamics of Sphingomyelin Bilayer: Insight Gained through Systematic Comparison to Phosphatidylcholine [My Copy] Biophys. J., Vol. 87, No. 5. (1 November 2004), pp. 2976-2989. by Perttu Niemela, Marja T. Hyvonen, Ilpo Vattulainen posted to md membrane by robertvacha on 2008-06-20 17:30:41 as along with 1 person softsimu
	Molecular dynamics simulation of a palmitoyl-oleoyl phosphatidylserine bilayer with Na+ counterions and NaCl. [My Copy] Biophys J, Vol. 86, No. 3. (March 2004), pp. 1601-1609. by P. Mukhopadhyay, L. Monticelli, D. P. Tieleman posted to md membrane by robertvacha on 2008-06-20 17:29:24 as along with 3 people dimka easybakemuffin softsimu
	A Molecular Dynamics Study of the Pores Formed by Escherichia coli OmpF Porin in a Fully Hydrated Palmitoyloleoylphosphatidylcholine Bilayer [My Copy] Biophys. J., Vol. 74, No. 6. (1 June 1998), pp. 2786-2801. by D. P. Tieleman, H. J. . C. Berendsen posted to md membrane by robertvacha on 2008-06-20 17:28:35 as along with 1 person softsimu
	Alamethicin helices in a bilayer and in solution: molecular dynamics simulations. [My Copy] Biophysical journal, Vol. 76, No. 1 Pt 1. (January 1999), pp. 40-49. by D. P. Tieleman, M. S. Sansom, H. J. Berendsen posted to md membrane by robertvacha on 2008-06-20 17:27:43 as
	Molecular dynamics simulations of a fluid bilayer of dipalmitoylphosphatidylcholine at full hydration, constant pressure, and constant temperature. [My Copy] Biophysical journal, Vol. 72, No. 5. (May 1997), pp. 2002-2013. by O. Berger, O. Edholm, F. Jähnig posted to md membrane by robertvacha on 2008-06-20 17:24:58 as along with 3 people and 1 group choonpeng Marine sunnytov Molecular dynamics in MSU
	Phospholipids in animal eukaryotic membranes: transverse asymmetry and movement. [My Copy] Biochem J, Vol. 294 ( Pt 1) (15 August 1993), pp. 1-14. by A. Zachowski posted to asymmetry membrane by robertvacha on 2008-06-20 17:22:59 as along with 2 people davidng aminaikeno
	Settle: An analytical version of the SHAKE and RATTLE algorithm for rigid water models [My Copy] Journal of Computational Chemistry, Vol. 13, No. 8. (1992), pp. 952-962. by Shuichi Miyamoto, Peter A. Kollman posted to gromacs md by robertvacha on 2008-06-20 17:19:49 as along with 8 people oteri Lombardo_7 choonpeng A_Coletta_Thesis jwagoner tji softsimu ashaytan
	GROMACS: fast, flexible, and free. [My Copy] Journal of computational chemistry, Vol. 26, No. 16. (December 2005), pp. 1701-1718. by David Van Der Spoel, Erik Lindahl, Berk Hess, Gerrit Groenhof, Alan E. Mark, Herman J. Berendsen posted to gromacs by robertvacha on 2008-06-20 17:13:38 as along with 20 people and 2 groups arifor krapnik r2s2 janneb dsmueller oteri choonpeng sebk dimka jwm ttjoseph bilab rabio Dinler tji softsimu ashaytan sunnytov Diego_Prada A_Coletta_Thesis Radiation_Damage Stressosome
	GROMACS: A message-passing parallel molecular dynamics implementation [My Copy] Computer Physics Communications, Vol. 91, No. 1-3. (02 September 1995), pp. 43-56. by H. Berendsen posted to gromacs by robertvacha on 2008-06-20 17:11:56 as along with 7 people trishul xiaoshijun janneb choonpeng ffranca tji gisle
	Effects of monovalent anions of the hofmeister series on DPPC lipid bilayers Part II: modeling the perpendicular and lateral equation-of-state. [My Copy] Biophys. J., Vol. 93, No. 5. (2007), pp. 1591-607. by E. Leontidis, A. Aroti, L. Belloni, M. Dubois, T. Zemb posted to membrane-ions by robertvacha on 2008-06-20 10:45:12 as

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robertvacha's library 149 articles Export

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