Tag ab_initio [40 articles] Export

Recent papers classified by the tag ab_initio.

	All-atom ab initio native structure prediction of a mixed fold (1FME): a comparison of structural and folding characteristics of various beta beta alpha miniproteins. [My Copy] The Journal of chemical physics, Vol. 131, No. 19. (21 November 2009) by Eunae Kim, Soonmin Jang, Youngshang Pak posted to solvation protein_structure molecular_dynamics folding_algorithm folding energy_function all_atom ab_initio by melo_mcr on 2009-12-09 14:00:22 as
	Weakly correlated one-dimensional indium chains on Si(111) [My Copy] Physical Review B, Vol. 64, No. 23. (Nov 2001), 235302. by Jun H. Cho, Dong H. Oh, Kwang S. Kim, Leonard Kleinman posted to surface-physics silicon nanowire in-on-si111 dipc2 ab_initio 8x2 4x2 4x1 by agendafisica on 2009-11-26 14:47:04 as
	Electronic structure of one-dimensional indium chains on Si(111) [My Copy] Physical Review B, Vol. 71, No. 8. (Feb 2005), 081310. by Jun H. Cho, Jung Y. Lee, Leonard Kleinman posted to surface-physics simulated-stm nanowire in-on-si111 dipc2 ab_initio 4x1 by agendafisica on 2009-11-26 14:42:01 as
	First-principles calculation of the atomic structure of one-dimensional indium chains on Si(111): Convergence to a metastable structure [My Copy] Physical Review B (Condensed Matter and Materials Physics), Vol. 76, No. 3. (2007), 033405. by Jun H. Cho, Jung Y. Lee posted to surface-physics silicon nanowire in-on-si111 gga ab_initio 4x2 by agendafisica on 2009-11-26 14:30:12 as
	Dual folding pathways of an alpha/beta protein from all-atom ab initio folding simulations. [My Copy] The Journal of chemical physics, Vol. 131, No. 16. (28 October 2009) by Hongxing Lei, Zhi-Xiang X. Wang, Chun Wu, Yong Duan posted to protein_structure pathways folding energy_function all_atom ab_initio by melo_mcr on 2009-11-18 12:58:16 as
	Band offsets of HfO[sub 2]/ZnO interface: In situ x-ray photoelectron spectroscopy measurement and ab initio calculation [My Copy] Applied Physics Letters, Vol. 95, No. 16. (2009), 162104. by Q. Chen, M. Yang, Y. P. Feng, et al.J. W. Chai, Z. Zhang, J. S. Pan, S. J. Wang posted to x_ray_photoelectron_spectroscopy offsets ab_initio by JohnnyP on 2009-11-06 10:34:24 as
	Optical anisotropy of the In/Si(111)(4×1)/(8×2) nanowire array [My Copy] Surface Science, Vol. 603, No. 1. (01 January 2009), pp. 247-250. by S. Wippermann, W. Schmidt posted to trimer nanowire ab_initio 8x2 4x2 4x1 by agendafisica on 2009-11-04 14:02:22 as
	Ab initio correlation effects on the electronic and transport properties of metal(II)-phthalocyanine-based devices [My Copy] Nanotechnology, Vol. 18, No. 42. (2007), 424013. by Arrigo Calzolari, Andrea Ferretti, Marco B. Nardelli posted to phthalocyanines correlation_effects ab_initio by garjey on 2009-10-06 10:55:55 as
	Metal phthalocyanine ground states: covalence and ab initio calculation of spin and charge densities [My Copy] Inorganic Chemistry, Vol. 30, No. 10. (1 May 1991), pp. 2294-2300. by Philip A. Reynolds, Brian N. Figgis posted to structure electronic ab_initio by garjey on 2009-10-06 10:53:20 as
	<i>Ab initio</i> pair potential energy curve for the argon atom pair and thermophysical properties of the dilute argon gas. I. Argonargon interatomic potential and rovibrational spectra [My Copy] Molecular Physics: An International Journal at the Interface Between Chemistry and Physics, Vol. 107, No. 20. (2009), pp. 2181-2188. by Benjamin Jäger, Robert Hellmann, Eckard Bich, Eckhard Vogel posted to potential_energy argon_gas ab_initio by flbarroso on 2009-09-28 20:53:58 as
	Ab initio study of the optical absorption and wave-vector-dependent dielectric response of graphite [My Copy] Physical Review B, Vol. 69, No. 24. (Jun 2004), 245419. by A. G. Marinopoulos, Lucia Reining, Angel Rubio, Valerio Olevano posted to ab_initio diel_function graphite by georgwachter on 2009-08-07 14:02:39 as
	Recent advances in single-asperity nanotribology [My Copy] Journal of Physics D: Applied Physics, Vol. 41, No. 12. (2008), 123001. by Izabela Szlufarska, Michael Chandross, Robert W. Carpick posted to ab_initio friction review by Boxus on 2009-07-06 07:19:25 as along with 1 person ngosvami
	Ripples in epitaxial graphene on the Si-terminated SiC(0001) surface [My Copy] Physical Review B (Condensed Matter and Materials Physics), Vol. 77, No. 23. (2008) by F. Varchon, P. Mallet, J. Y. Veuillen, L. Magaud posted to ab_initio graphene stm by Boxus on 2009-05-28 12:30:14 as along with 1 person kas
	Calculation of electronic stopping power along glancing swift heavy ion tracks in perovskites using ab initio electron density data [My Copy] Journal of Physics: Condensed Matter, Vol. 20, No. 31. (2008), 315001. by O. Osmani, A. Duvenbeck, E. Akcöltekin, R. Meyer, H. Lebius, M. Schleberger posted to ab_initio electronic_stopping glancing surface swift_heavy_ions by georgwachter on 2008-09-09 11:51:27 as
	First-principles calculations of the CaF<SUB><FONT SIZE='-1'>2</FONT></SUB> bulk and surface electronic structure [My Copy] physica status solidi (b), Vol. 242, No. 10. (2005), pp. 2041-2050. by H. Shi, R. I. Eglitis, G. Borstel posted to ab_initio bulk electronic_structure surface by georgwachter on 2008-09-09 11:21:51 as
	Surface erosion and modification by highly charged ions [My Copy] Physical Review A (Atomic, Molecular, and Optical Physics), Vol. 77, No. 6. (2008) by Z. Insepov, M. Terasawa, K. Takayama posted to ab_initio caf2 electronic_structure hillocks md model by georgwachter on 2008-09-09 11:17:09 as
	Ab initio calculations of the CaF[sub 2] electronic structure and F centers [My Copy] Physical Review B (Condensed Matter and Materials Physics), Vol. 72, No. 4. (2005) by H. Shi, R. I. Eglitis, G. Borstel posted to ab_initio caf2 electronic_structure by georgwachter on 2008-09-09 11:06:40 as
	Determination of Compton profiles at solid surfaces from first-principles calculations [My Copy] Physical Review B (Condensed Matter and Materials Physics), Vol. 75, No. 1. (2007), 014303. by Christoph Lemell, Andres Arnau, Joachim Burgdörfer posted to ab_initio compton_profile group by georgwachter on 2008-09-08 15:34:24 as
	First-principles calculation of the electronic, dielectric, and dynamical properties of CaF\subscript2 [My Copy] Physical Review B, Vol. 68, No. 19. (26 November 2003), 195123. by Matthieu Verstraete, Xavier Gonze posted to ab_initio caf2 by georgwachter on 2008-09-08 15:32:49 as
	Superhard Materials [My Copy] physica status solidi (b), Vol. 217, No. 1. (2000), pp. 533-543. by J. E. Lowther posted to ab_initio superhard_materials by driver on 2008-08-09 22:06:29 as
	Extending the treatment of backbone energetics in protein force fields: Limitations of gas-phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations [My Copy] Journal of Computational Chemistry, Vol. 25, No. 11. (2004), pp. 1400-1415. by Alexander D. Mackerell, Michael Feig, Charles L. Brooks posted to ab_initio charmm dipeptides force_field by middledomain on 2008-08-01 09:30:33 as along with 4 people tovrstra mkrishna dgront hlwoodcock
	High-pressure behavior of MgO: Structural and electronic properties [My Copy] Physical Review B, Vol. 30, No. 8. (15 October 1984), 4774. by K. J. Chang, Marvin L. Cohen posted to ab_initio dft lda mgo transition_pressure by driver on 2008-07-30 16:09:42 as
	Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and bayesian scoring functions [My Copy] Journal of Molecular Biology, Vol. 268, No. 1. (25 April 1997), pp. 209-225. by K. Simons posted to ab_initio protein rosetta by joule on 2008-07-22 16:18:52 as along with 12 people and 2 groups chemrahul82 paddydu Diego_Prada reyez guxiyou ana jwm vavi wouterboomsma j3xucite hmk mijam structural_bioinformatics Bioinformatics
	Quantum Mechanical Computations and Spectroscopy: From Small Rigid Molecules in the Gas Phase to Large Flexible Molecules in Solution [My Copy] Acc. Chem. Res. (29 February 2008) by Vincenzo Barone, Roberto Improta, Nadia Rega posted to ab_initio epr ir nmr review by middledomain on 2008-02-29 10:23:39 as along with 3 people and 1 group A_Coletta_Thesis yzlab paulschlesinger Structural Biology Group TorVergata
	CisModule: De novo discovery of cis-regulatory modules by hierarchical mixture modeling [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 101, No. 33. (17 August 2004), pp. 12114-12119. by Qing Zhou, Wing H. Wong posted to ab_initio cis_regulatory_elements clustering method prediction by dpollard to the group EisenLab on 2007-12-05 22:46:33 as along with 4 people tonamswish isimpson indigoviolet ep161302
	High-resolution structure prediction and the crystallographic phase problem [My Copy] Nature, Vol. 450, No. 7167. (14 October 2007), pp. 259-264. by Bin Qian, Srivatsan Raman, Rhiju Das, et al.Philip Bradley, Airlie J. McCoy, Randy J. Read, David Baker posted to ab_initio crystallography nmr prediction protein star3 structure x-ray by eckart_bindewald on 2007-11-19 12:47:07 as along with 16 people and 2 groups bmduggan newton1234 apaydin aheilbut jwm ffranca dgront massivemayhem cjeans zwang cactus sobolevnrm boris_aguilar Ema chenway ardalby baker-group OPIG
	Discovery of Regulatory Elements by a Computational Method for Phylogenetic Footprinting [My Copy] Genome Res., Vol. 12, No. 5. (1 May 2002), pp. 739-748. by Mathieu Blanchette, Martin Tompa posted to ab_initio binding_site conservation method prediction by dpollard to the group EisenLab on 2007-11-01 00:41:11 as along with 7 people and 1 group wowalz coldmeadow chad_davis balajis lyongu dquest csdhwang cis-regulatory-evolution
	Regulatory element detection using correlation with expression [My Copy] Nature Genetics, Vol. 27, No. 2. (01 February 2001), pp. 167-174. by Harmen J. Bussemaker, Hao Li, Eric D. Siggia posted to ab_initio binding_site gene_expression prediction by dpollard to the group EisenLab on 2007-11-01 00:10:36 as along with 5 people and 1 group roys nickluscombe heliopais tvdbulck isimpson EBI-regulation
	Systematic detection of statistically overrepresented DNA motif association rules. [My Copy] Genome Inform, Vol. 17, No. 1. (2006), pp. 124-133. by J. M. Lin, Z. Weng posted to ab_initio binding_site eisen_journal_club method motif_detection prediction round_robin rules venky_presented by dpollard on 2007-06-15 00:04:13 as along with 1 person and 1 group indigoviolet EisenLab
	Binding Site Graphs: A New Graph Theoretical Framework for Prediction of Transcription Factor Binding Sites [My Copy] PLoS Comput Biol, Vol. 3, No. 5. (11 May 2007), e90. by Timothy E. Reddy, Charles DeLisi, Boris E. Shakhnovich posted to ab_initio binding_site eisen_journal_club method motif round_robin venky_presented yeast by dpollard on 2007-06-14 23:38:43 as along with 7 people and 1 group pradiptaray nklee aalibes medic0747 GustavoLacerda mircea marti EisenLab
	Determination of local statistical significance of patterns in Markov sequences with application to promoter element identification. [My Copy] J Comput Biol, Vol. 11, No. 1. (2004), pp. 1-14. by H. Huang, M. C. Kao, X. Zhou, J. S. Liu, W. H. Wong posted to stuart_presented round_robin motif method markov eisen_journal_club binding_site ab_initio by dpollard to the group EisenLab on 2007-06-04 22:47:45 as along with 1 person jguinney
	Global Discriminative Learning for Higher-Accuracy Computational Gene Prediction [My Copy] PLoS Computational Biology, Vol. 3, No. 3. (1 March 2007), e54. by Axel Bernal, Koby Crammer, Artemis Hatzigeorgiou, Fernando Pereira posted to ab_initio gene_prediction method by dpollard on 2007-03-23 00:33:15 as along with 1 person and 1 group GustavoLacerda EisenLab
	Global Discriminative Learning for Higher-Accuracy Computational Gene Prediction [My Copy] PLoS Computational Biology, Vol. 3, No. 3. (1 March 2007), e54. by Axel Bernal, Koby Crammer, Artemis Hatzigeorgiou, Fernando Pereira posted to ab_initio gene_prediction method by dpollard on 2007-03-16 21:10:40 as along with 5 people and 2 groups dakelley wenhan zwang acarbo alexl Bioinformatics EisenLab
	Long loop prediction using the protein local optimization program. [My Copy] Proteins (22 August 2006) by Kai Zhu, David L L. Pincus, Suwen Zhao, Richard A A. Friesner posted to ab_initio loop_prediction protein by vavi on 2006-08-28 09:32:33 as along with 2 people mijam cdeane
	A divide and conquer approach to fast loop modeling [My Copy] Protein Eng., Vol. 15, No. 4. (1 April 2002), pp. 279-286. by Silvio C. Tosatto, Eckart Bindewald, Jurgen Hesser, Reinhard Manner posted to ab_initio loop_modeling protein by vavi on 2006-07-31 10:31:02 as
	Prediction of loop geometries using a generalized born model of solvation effects [My Copy] Proteins: Structure, Function, and Genetics, Vol. 35, No. 2. (1999), pp. 173-183. by Chaya S. Rapp, Richard A. Friesner posted to ab_initio molecular_dynamics monte_carlo protein structure_prediction by vavi on 2006-07-31 09:23:54 as
	Exploratory studies of ab initio protein structure prediction: multiple copy simulated annealing, AMBER energy functions, and a generalized born/solvent accessibility solvation model. [My Copy] Proteins, Vol. 46, No. 1. (1 January 2002), pp. 128-146. by Y. Liu, D. L. Beveridge posted to ab_initio molecular_dynamics monte_carlo protein simulated_annealing structure_prediction by vavi on 2006-07-31 09:00:25 as along with 1 person flbarroso
	Ab initio protein structure prediction: progress and prospects. [My Copy] Annual review of biophysics and biomolecular structure, Vol. 30 (2001), pp. 173-189. by R. Bonneau, D. Baker posted to ab_initio protein review structure_prediction by vavi on 2006-07-25 14:29:29 as along with 2 people flbarroso dgront
	Ab initio modeling of small, medium, and large loops in proteins [My Copy] Peptide Science, Vol. 60, No. 2. (6 July 2001), pp. 153-168. by Stan Galaktionov, Gregory V. Nikiforovich, Garland R. Marshall posted to ab_initio contact_map loop_prediction protein by vavi on 2005-11-07 15:54:00 as
	Have we seen all structures corresponding to short protein fragments in the Protein Data Bank? An update. [My Copy] Protein Eng, Vol. 16, No. 6. (June 2003), pp. 407-414. by P. Du, M. Andrec, R. M. Levy posted to 15872 ab_initio fragment_approach structure_prediction by karbak on 2005-01-18 23:19:55 as along with 3 people apaydin thaliana vavi

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nanowire	20
silicon	14
method	13
quantum_confinement	11
binding_site	9
defect	9
band_structure	8
prediction	8
protein	8
diameter	5
eisen_journal_club	5
round_robin	5
theoric	5
gene_prediction	4
motif	4
structure_prediction	4
surface_segregation	4
4x1	3
4x2	3
caf2	3
electronic_structure	3
in-on-si111	3
molecular_dynamics	3
review	3
surface-physics	3
venky_presented	3
8x2	2
all_atom	2
cis_regulatory_elements	2
clustering	2
conservation	2
deactivation	2
dielectric_confinement	2
dipc2	2
energy_function	2
folding	2
formation_energies	2
gene_expression	2
loop_prediction	2
markov	2
monte_carlo	2
nanocrystal	2
nmr	2
orientation	2
passivation	2
protein_structure	2
structure	2
stuart_presented	2
surface	2
yeast	2
15872	1
amino_acid_sequences	1
band_folding	1
charmm	1
compton_profile	1
contact_map	1
crystallography	1
dft	1
diel_function	1
dipeptides	1
effective_mass_approx	1
epr	1
experimental	1
ferromagnetism	1
folding_algorithm	1
force_field	1
fragment_approach	1
friction	1
gga	1
glancing	1
graphene	1
graphite	1
group	1
ir	1
lda	1
modeling	1
motif_discovery	1
offsets	1
open_source_license	1
photoluminescence	1
phthalocyanines	1
porous_silicon	1
potential_energy	1
protein_motif	1
protein_motifs	1
rosetta	1
rules	1
section_shape	1
self_purification	1
simulated_annealing	1
solvation	1
star3	1
stm	1
surfaces	1
threading	1
tight_binding	1
transition_pressure	1
trimer	1
x-ray	1
x_ray_photoelectron_spectroscopy	1

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