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Northwest Biophysics Consortium
Publication Listing for Alexey Savelyev
- GenApp: Extensible tool for rapid generation of web and native GUI applications
Savelyev, A.; Brookes E.
Future Generation Computer Systems: 2017-10-23; 94(1); 929-936
PMID: LINK: https://doi.org/10.1016/j.future.2017.09.069
- GenApp Integrated with OpenStack Supports Elastic Computing on Jetstream
Savelyev, A.; Brookes E.
AMC: 2017-07-09; ISBN: 978-1-4503-5272-7(1); 11
PMID: LINK: https://dl.acm.org/citation.cfm?doid=3093338.3093356
- Explicit Inclusion of Induced Polarization Effects in Atomistic Force Fields Based on the Classical Drude Oscillator Model
Savelyev, A.; B. Roux; Mackerell A. D.
Many-Body Effects and Electrostatics in Biomolecules. Pan Stanford Publishing: 2016-01-01; Print ISBN: 978-981-4613-92-7();
PMID: LINK: https://books.google.com/books?id=bsjXCwAAQBAJ&pg=PA191&lpg=PA191&dq=Explicit+Inclusion+of+Induced+Polarization+Effe
- Differential Deformability of the DNA Minor Groove and Altered BI/BII Backbone Conformational Equilibrium by the Monovalent Ions Li(+), Na(+), K(+), and Rb(+) via Water-Mediated Hydrogen Bonding.
Savelyev A, MacKerell AD Jr
J Chem Theory Comput: 2015-09-08; 11(9); 4473-85 Epub: 2015-08-26.
PMID: 26575937 LINK:
- Competition among Li(+), Na(+), K(+), and Rb(+) monovalent ions for DNA in molecular dynamics simulations using the additive CHARMM36 and Drude polarizable force fields.
Savelyev A, MacKerell AD Jr
J Phys Chem B: 2015-03-26; 119(12); 4428-40 Epub: 2015-03-18.
PMID: 25751286 LINK:
- Differential Impact of the Monovalent Ions Li⁺, Na⁺, K⁺, and Rb⁺ on DNA Conformational Properties.
Savelyev A, MacKerell AD Jr
J Phys Chem Lett: 2015-01-02; 6(1); 212-6
PMID: 25580188 LINK:
- Induced Polarization Influences the Fundamental Forces in DNA Base Flipping.
Lemkul JA, Savelyev A, MacKerell AD Jr
J Phys Chem Lett: 2014-06-19; 5(12); 2077-2083 Epub: 2014-05-28.
PMID: 24976900 LINK:
- Balancing the interactions of ions, water, and DNA in the Drude polarizable force field.
Savelyev A, MacKerell AD Jr
J Phys Chem B: 2014-06-19; 118(24); 6742-57 Epub: 2014-06-09.
PMID: 24874104 LINK:
- All-atom polarizable force field for DNA based on the classical Drude oscillator model.
Savelyev A, MacKerell AD Jr
J Comput Chem: 2014-06-15; 35(16); 1219-39 Epub: 2014-04-18.
PMID: 24752978 LINK:
- Recent successes in coarse-grained modeling of DNA.
Potoyan, D. A.; Savelyev, A.; Papoian, G. A
WIREs Comput. Mol. Sci.: 2013-01-01; 3(1); 69-83
PMID: LINK: https://onlinelibrary.wiley.com/doi/abs/10.1002/wcms.1114
- Do monovalent mobile ions affect DNA's flexibility at high salt content?
Savelyev A
Phys Chem Chem Phys: 2012-02-21; 14(7); 2250-4 Epub: 2012-01-13.
PMID: 22246071 LINK:
- Is DNA's rigidity dominated by electrostatic or nonelectrostatic interactions?
Savelyev A, Materese CK, Papoian GA
J Am Chem Soc: 2011-12-07; 133(48); 19290-3 Epub: 2011-11-11.
PMID: 22039974 LINK:
- Nonequilibrium water transport in a nonionic microemulsion system.
Minakova M, Savelyev A, Papoian GA
J Phys Chem B: 2011-05-26; 115(20); 6503-8 Epub: 2011-04-29.
PMID: 21528855 LINK:
- Chemically accurate coarse graining of double-stranded DNA.
Savelyev A, Papoian GA
Proc Natl Acad Sci U S A: 2010-11-23; 107(47); 20340-5 Epub: 2010-11-08.
PMID: 21059937 LINK:
- Counterion atmosphere and hydration patterns near a nucleosome core particle.
Materese CK, Savelyev A, Papoian GA
J Am Chem Soc: 2009-10-21; 131(41); 15005-13
PMID: 19778017 LINK:
- Molecular renormalization group coarse-graining of electrolyte solutions: application to aqueous NaCl and KCl.
Savelyev A, Papoian GA
J Phys Chem B: 2009-06-04; 113(22); 7785-93
PMID: 19425537 LINK:
- Molecular renormalization group coarse-graining of polymer chains: application to double-stranded DNA.
Savelyev A, Papoian GA
Biophys J: 2009-05-20; 96(10); 4044-52
PMID: 19450476 LINK:
- Polyionic charge density plays a key role in differential recognition of mobile ions by biopolymers.
Savelyev A, Papoian GA
J Phys Chem B: 2008-07-31; 112(30); 9135-45 Epub: 2008-07-03.
PMID: 18597519 LINK:
- Inter-DNA electrostatics from explicit solvent molecular dynamics simulations.
Savelyev A, Papoian GA
J Am Chem Soc: 2007-05-16; 129(19); 6060-1 Epub: 2007-04-25.
PMID: 17455935 LINK:
- Free energy calculations of counterion partitioning between DNA and chloride solutions
Alexey Savelyev, Garegin A Papoian
Mendeleev Communications: 2007-03-01; 17(2); 97-99
PMID: LINK: https://www.sciencedirect.com/science/article/pii/S0959943607000442
- Electrostatic, steric, and hydration interactions favor Na(+) condensation around DNA compared with K(+).
Savelyev A, Papoian GA
J Am Chem Soc: 2006-11-15; 128(45); 14506-18
PMID: 17090034 LINK:
- Theory of microphase separation in homopolymer-oligomer mixtures
Olemskoi A. I.; Savelyev A.
Physic Reports: 2005-11-01; 419(4-5); 145-205
PMID: LINK: https://www.sciencedirect.com/science/article/abs/pii/S0370157305003297
- Theory of homopolymer–oligomer microphase separation
Alexander Olemskoi, Ivan Krakovsky, Alexey Savelyev
Physica A: Statistical Mechanics and its Applications: 2004-04-15; 335(3-4); 554-562
PMID: LINK: https://www.sciencedirect.com/science/article/pii/S0378437103011129
- Supersymmetry theory of microphase separation in homopolymer-oligomer mixtures.
Olemskoi A, Krakovsky I, Savelyev A
Phys Rev E Stat Nonlin Soft Matter Phys: 2004-02-01; 69(2 Pt 1); 021803 Epub: 2004-02-17.
PMID: 14995479 LINK: