DNA nanotechnology: understanding and optimisation through simulation
By: Ouldridge, Thomas E.
MOLECULAR PHYSICS Volume: 113 Issue: 1 Pages: 1-15 Published: JAN 2 2015
- 2014
Simulating a burnt-bridges DNA motor with a coarse-grained DNA model
By: Sulc, Petr; Ouldridge, Thomas E.; Romano, Flavio; et al.
NATURAL COMPUTING Volume: 13 Special Issue: SI Pages: 535-547 Part: 1-2
DNA Duplex Formation with a Coarse-Grained Model
By: Maciejczyk, Maciej; Spasic, Aleksandar; Liwo, Adam; et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION Volume: 10 Pages: 5020-5035
By: Freeman, Gordon S.; Hinckley, Daniel M.; Lequieu, Joshua P.; et al.
JOURNAL OF CHEMICAL PHYSICS Volume: 141 Issue: 16 Article Number: 165103
A polarizable coarse-grained water model for dissipative particle dynamics
By: Peter, Emanuel K.; Pivkin, Igor V.
JOURNAL OF CHEMICAL PHYSICS Volume: 141 Issue: 16 Article Number: 164506
By: Le, Tung T.; Kim, Harold D.
NUCLEIC ACIDS RESEARCH Volume: 42 Pages: 10786-U807
Close encounters with DNA
By: Maffeo, C.; Yoo, J.; Comer, J.; et al.
JOURNAL OF PHYSICS-CONDENSED MATTER Volume: 26 Article Number: 413101
JOURNAL OF PHYSICS-CONDENSED MATTER Volume: 26 Article Number: 413101
The Treatment of Solvent in Multiscale Biophysical Modeling
By: Lazaridis, Themis; Versace, Rodney
By: Lazaridis, Themis; Versace, Rodney
By: Goyal, Puja; Qian, Hu-Jun; Irle, Stephan; et al.
JOURNAL OF PHYSICAL CHEMISTRY B Volume: 118 Pages: 11007-11027
JOURNAL OF PHYSICAL CHEMISTRY B Volume: 118 Pages: 11007-11027
Direct Mixing of Atomistic Solutes and Coarse-Grained Water
By:Mario Orsi, Wei Ding, and Michail Palaiokostas
JOURNAL OF CHEMICAL THEORY AND COMPUTATION Volume: 10 Pages: 4684−4693.
Coarse-Graining of TIP4P/2005, TIP4P-Ew, SPC/E, and TIP3P to Monatomic Anisotropic Water Models Using Relative Entropy Minimization
By: Lu, Jibao; Qiu, Yuqing; Baron, Riccardo; et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION Volume: 10 Issue: 9 Pages: 4104-4120.
A Coarse-Grained Model of Unstructured Single-Stranded DNA Derived from Atomistic Simulation and Single-Molecule Experiment
By: Maffeo, Christopher; Ngo, Thuy T. M.; Ha, Taekjip; et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION Volume: 10 Issue: 8 Pages: 2891-2896.
Coarse-grained modeling of DNA oligomer hybridization: Length, sequence, and salt effects
By: Hinckley, Daniel M.; Lequieu, Joshua P.; de Pablo, Juan J.
JOURNAL OF CHEMICAL PHYSICS Volume: 141 Issue: 3 Article Number: 035102.
Denaturation and renaturation behaviors of short DNA in a confined space
By: Li, Huaping; Wang, Zilu; Li, Ningning; et al.
JOURNAL OF CHEMICAL PHYSICS Volume: 141 Issue: 4 Article Number: 044911.
A Solvent-Mediated Coarse-Grained Model of DNA Derived with the Systematic Newton Inversion Method
By: Naome, Aymeric; Laaksonen, Aatto; Vercauteren, Daniel P.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION Volume: 10 Issue: 8 Pages: 3541-3549.
Adaptive Resolution Simulation of MARTINI Solvents
By: Zavadlav, Julija; Melo, Manuel N.; Cunha, Ana V.; et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION Volume: 10 Issue: 6 Pages: 2591-2598
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Jacobson, LC.; Kirby, RM.; Molinero, V.
JOURNAL OF PHYSICAL CHEMISTRY B 2014, 118: 8190-8202
How Short Is Too Short for the Interactions of a Water Potential? Exploring the Parameter Space of Coarse-Grained Water Model Using Uncertainty Quantification.
Korolev, N; Luo, D; Lyubartsev, AP.; Nordenskioeld, L
POLYMERS 2014, 6:
1655-1675
A Coarse-Grained DNA Model Parameterized from Atomistic Simulations by Inverse Monte CarloDi Pasquale, N.; Gowers, RJ.; Carbone, P.
JOURNAL OF COMPUTATIONAL CHEMISTRY 2014, 35: 1199-1207
A Multiple Time Step Scheme for Multiresolved Models of Macromolecules
Shen, L.; Hu, H.
Resolution-Adapted All-Atomic and Coarse-Grained Model for Biomolecular Simulation
Zavadlav, J.; Melo, MN; Marrink, SJ.; et al.
JOURNAL OF CHEMICAL PHYSICS 2014, 140: 054114
Adaptive resolution simulation of an atomistic protein in MARTINI water
Frederickx, R.; in't Veld, T.; Carlon, E.
PHYSICAL REVIEW LETTERS 2014, 112: 198102.
Anomalous Dynamics of DNA Hairpin Folding
Howard, JC.; Tschumper, S.
WILEY INTERDISCIPLINARY REVIEWS-COMP. MOLECULAR SCIENCE 2014, 4:199
Wavefunction methods for the accurate characterization of water clusters
Braun, D.; Boresch, S.; Steinhauser, O.
JOURNAL OF CHEMICAL PHYSICS, 2014, 140, 064107
Transport and dielectric properties of water and the influence of coarse-graining: Comparing BMW, SPC/E, and TIP3P models
Fogarty, JC.; Chiu, SW.; Kirby, P.
JOURNAL OF PHYSICAL CHEMISTRY B, 2014, 118, 1603
Automated Optimization of Water-Water Interaction Parameters for a Coarse-Grained Model
Zavadlav, J.; Melo, MN. Marrink; SJ., Praprotnik, M.
JOURNAL OF CHEMICAL PHYSICS, 2014, 140, 054114.
Adaptive resolution simulation of an atomistic protein in MARTINI water
Yadava, RM; Yadava, U.
Medicinal Chemistry Research, 2014, 23, 280
Molecular dynamics simulation of DNA duplex, analog of PPT (polypurine tract), its conformation and hydration: a theoretical study
Leherte, L., Vercauteren, DP.
Journal of Molecular Graphics and Modelling, 2014, 47: 44
Evaluation of reduced point charge models of proteins through Molecular Dynamics simulations: Application to the Vps27 UIM-1–Ubiquitin complex
- 2013
Wang, Q; Suzuki, K; Nagashima, U; Tachikawa, M; Yan, S.
CHEMICAL PHYSICS, 2013, 426:38
Geometric isotope effects on small chloride ion water clusters with path integral molecular dynamics simulations
Hinckley, DM; Freeman, GS; Whitmer, JK; de Pablo, JJ.
J. Chem. Phys. 2013, 139, 144903
An experimentally-informed coarse-grained 3-site-per-nucleotide model of DNA: Structure, thermodynamics, and dynamics of hybridization
Noid, W. G.
J. Chem. Phys. 2013, 139, 090901
Perspective: Coarse-grained models for biomolecular systems.
T. Cragnolini, P. Derreumaux, S. Pasquali.
J. Phys. Chem. B 2013, 117:8047.
Ouldridge, TE; Sulc, P; Romano, F; Doye, JPK;Louis, AA.
NUCLEIC ACIDS RESEARCH 2013, 41:8886
DNA hybridization kinetics: zippering, internal displacement and sequence dependence.
Spillmann, CM; Ancona, MG; Buckhout-White, S; Algar, R; Stewart, MH; Susumu, K; Huston, AL;Goldman, ER; Igor L. Medintz, IL.
ACS Nano, 2013, 7, 8:7101
Achieving Effective Terminal Exciton Delivery in Quantum Dot Antenna-Sensitized Multistep DNA Photonic Wires.
Sokkar,P; Choi, SM; Rhee, YM.
JCTC, 2013, 9, 3778
Simple Method for Simulating the Mixture of Atomistic and Coarse- Grained Molecular Systems.
Spiga, E; Alemani, D; Degiacomi, MT; Cascella, M; Dal Peraro, M.
JCTC, 2013, 9, 3515
Electrostatic-Consistent Coarse-Grained Potentials for Molecular
Simulations of Proteins.
Ingolfsson, HI; Lopez, CA; Uusitalo, JJ; de Jong, DH; Gopal, SM; Periole, X; Marrink, SJ.
WIREs Computational Molecular Science. 2013 DOI: 10.1002/wcms.1169
Wang, Q; Suzuki, K; Nagashima, U; Tachikawa, M; Yan, S.
CHEMICAL PHYSICS, 2013, 426:38
Geometric isotope effects on small chloride ion water clusters with path integral molecular dynamics simulations
Hinckley, DM; Freeman, GS; Whitmer, JK; de Pablo, JJ.
J. Chem. Phys. 2013, 139, 144903
An experimentally-informed coarse-grained 3-site-per-nucleotide model of DNA: Structure, thermodynamics, and dynamics of hybridization
Noid, W. G.
J. Chem. Phys. 2013, 139, 090901
Perspective: Coarse-grained models for biomolecular systems.
T. Cragnolini, P. Derreumaux, S. Pasquali.
J. Phys. Chem. B 2013, 117:8047.
Coarse-grained simulations of RNA and DNA duplexes.
NUCLEIC ACIDS RESEARCH 2013, 41:8886
DNA hybridization kinetics: zippering, internal displacement and sequence dependence.
Spillmann, CM; Ancona, MG; Buckhout-White, S; Algar, R; Stewart, MH; Susumu, K; Huston, AL;Goldman, ER; Igor L. Medintz, IL.
ACS Nano, 2013, 7, 8:7101
Achieving Effective Terminal Exciton Delivery in Quantum Dot Antenna-Sensitized Multistep DNA Photonic Wires.
Sokkar,P; Choi, SM; Rhee, YM.
JCTC, 2013, 9, 3778
Simple Method for Simulating the Mixture of Atomistic and Coarse- Grained Molecular Systems.
Spiga, E; Alemani, D; Degiacomi, MT; Cascella, M; Dal Peraro, M.
JCTC, 2013, 9, 3515
Electrostatic-Consistent Coarse-Grained Potentials for Molecular
Simulations of Proteins.
Ingolfsson, HI; Lopez, CA; Uusitalo, JJ; de Jong, DH; Gopal, SM; Periole, X; Marrink, SJ.
WIREs Computational Molecular Science. 2013 DOI: 10.1002/wcms.1169
The power of coarse graining in biomolecular simulations.
Dasanna, AK; Destainville, N; Palmeri, J; et al.
PHYSICAL REVIEW E Vol: 87 Art. Number: 052703
Slow closure of denaturation bubbles in DNA: Twist matters.
Slow closure of denaturation bubbles in DNA: Twist matters.
Wassenaar, TA; Ingolfsson, HI; Priess, M; Marrink, SJ; Schafer, LV.
Fan, Y.; Korolev, N.; Lyubartsev, A.; Nordenskiold, L.
PLOS ONE, Vol:8 Art. Number: e54228
An Advanced Coarse-Grained Nucleosome Core Particle Model for Computer Simulations of Nucleosome-Nucleosome Interactions under Varying Ionic Conditions
Gonzalez, O.; Petkeviciute, D.; Maddocks, J. H.
J. CHEM. PHYS., Vol: 138 Art. Number: 035102
A sequence-dependent rigid-base model of DNA.
Basdevant, N; Borgis, D; Ha-Duong, T.
JCTC, Vol: 9 Pages: 803-813
Modeling Protein-Protein Recognition in Solution Using the Coarse-Grained Force Field SCORPION
Laurent, B; Murail, S; Da Silva, F; Corringer, PJ; Baaden, M.
PURE AND APPLIED CHEMISTRY Vol: 85 Pages: 1-13
Modeling complex biological systems: From solution chemistry to membranes and channels.
Schmitt, Terry J.; Rogers, J. Brandon; Knotts, Thomas A.
JOURNAL OF CHEMICAL PHYSICS 2013 Vol: 138 Art. Number: 035102
J. PHYS. CHEM. B, 2013, Vol:117 Pages: 3516–3530
Mixing MARTINI: Electrostatic Coupling in Hybrid Atomistic–Coarse-Grained Biomolecular Simulations
Fan, Y.; Korolev, N.; Lyubartsev, A.; Nordenskiold, L.
PLOS ONE, Vol:8 Art. Number: e54228
An Advanced Coarse-Grained Nucleosome Core Particle Model for Computer Simulations of Nucleosome-Nucleosome Interactions under Varying Ionic Conditions
Gonzalez, O.; Petkeviciute, D.; Maddocks, J. H.
J. CHEM. PHYS., Vol: 138 Art. Number: 035102
A sequence-dependent rigid-base model of DNA.
Basdevant, N; Borgis, D; Ha-Duong, T.
JCTC, Vol: 9 Pages: 803-813
Modeling Protein-Protein Recognition in Solution Using the Coarse-Grained Force Field SCORPION
Laurent, B; Murail, S; Da Silva, F; Corringer, PJ; Baaden, M.
PURE AND APPLIED CHEMISTRY Vol: 85 Pages: 1-13
Modeling complex biological systems: From solution chemistry to membranes and channels.
Schmitt, Terry J.; Rogers, J. Brandon; Knotts, Thomas A.
JOURNAL OF CHEMICAL PHYSICS 2013 Vol: 138 Art. Number: 035102
Exploring the mechanisms of DNA hybridization on a surface.
Edens, Lance E.; Brozik, James A.; Keller, David J.
JOURNAL OF PHYSICAL CHEMISTRY B 2013 Vol: 116 Pages: 14735-14743
JOURNAL OF PHYSICAL CHEMISTRY B 2013 Vol: 116 Pages: 14735-14743
Coarse-Grained Model DNA: Structure, Sequences, Stems, Circles, Hairpins.
- 2012
Spiriti, Justin; van der Vaart, Arjan
Vol: 3 Pages: 3029 DOI: 10.1021/jz301227y
DNA Bending through Roll Angles Is Independent of Adjacent Base Pairs
DNA Bending through Roll Angles Is Independent of Adjacent Base Pairs
di Pasquale, Nicodemo; Marchisio, Daniele; Carbone, Paola
JOURNAL OF CHEMICAL PHYSICS 2012
Vol: 137 Art. Number: 164111 DOI: 10.1063/1.4759504
Mixing atoms and coarse-grained beads in modelling polymer melts
JOURNAL OF CHEMICAL PHYSICS 2012
Vol: 137 Art. Number: 164111 DOI: 10.1063/1.4759504
Mixing atoms and coarse-grained beads in modelling polymer melts
Sulc, Petr; Romano, Flavio; Ouldridge, Thomas E.; Rovigatti, Lorenzo; Doye, Jonathan P.K; Louis, Ard A.
Vol: 137 Art. Number: 135101 DOI: 10.1063/1.4754132
Sequence-dependent thermodynamics of a coarse-grained DNA model
Hsu, Chia Wei; Fyta, Maria; Lakatos, Greg; Melchionna, Simone; Kaxiras, Efthimios
JOURNAL OF CHEMICAL PHYSICS 2012
Vol: 137 Art. Number: 105102 DOI: 10.1063/1.4748105
Ab initio determination of coarse-grained interactions in double-stranded DNA
Davit A. Potoyan, Alexey Savelyev, Garegin A. Papoian
WIREs Computational Molecular Science.
Filip Lankas
Modelling Nucleic Acid Structure and Flexibility: From Atomic to Mesoscopic Scale.
In "Innovations in Biomolecular Modeling and Simulations", 2012 RSC Publishing, ISBN: 978-1-84973-505-6
Chang, Rakwoo; Jo, Kyubong.
Aug. 2012 DOI: 10.1002/wcms.1114
Recent Successes in Coarse Grained Modelling of DNA
Filip Lankas
Modelling Nucleic Acid Structure and Flexibility: From Atomic to Mesoscopic Scale.
In "Innovations in Biomolecular Modeling and Simulations", 2012 RSC Publishing, ISBN: 978-1-84973-505-6
Chang, Rakwoo; Jo, Kyubong.
JOURNAL OF CHEMICAL PHYSICS 2012 Vol: 136
Art. Number: 095101.
DNA conformation in nanochannels: Monte Carlo
simulation studies using a primitive DNA model
Hadley, Kevin R.; McCabe, Clare.
MOLECULAR SIMULATION Vol: 38 Pages: 671-681
Coarse-grained molecular models of water: a
review
Wu, Zhe; Cui, Qiang; Yethiraj, Arun.
JOURNAL OF CHEMICAL THEORY AND
COMPUTATION Volume: 7 Pages: 3793-3802
DOI: 10.1021/ct200593t
A New Coarse-Grained Force Field for
Membrane-Peptide Simulations
Wu, Zhe; Cui, Qiang; Yethiraj, Arun.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS 2012
Volume: 2 Pages: 1794-1798
Driving Force for the Association of
Hydrophobic Peptides: The Importance of Electrostatic Interactions in
Coarse-Grained Water Models
Sim, Adelene Y. L.; Minary, Peter; Levitt,
Michael
CURRENT OPINION IN STRUCTURAL BIOLOGY 2012
Volume: 22 Pages: 273-278 DOI:
10.1016/j.sbi.2012.03.012
Modeling nucleic acids
Spiriti, Justin; Kamberaj, Hiqmet; de Graff,
Adam M. R.; et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
2012 Volume: 8 Pages: 2145-2156
DNA Bending through Large Angles Is Aided by
Ionic Screening
McCullagh, Martin; Franco, Ignacio; Ratner,
Mark A.; et al.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS 2012
Volume: 3 Pages: 689-693 DOI:
10.1021/jz201649k
Defects in DNA: Lessons from Molecular Motor
Design
Perez, Alberto; Javier Luque, F.; Orozco,
Modesto
ACCOUNTS OF CHEMICAL RESEARCH 2012 Volume: 45
Pages: 196-205
Frontiers in Molecular Dynamics Simulations of
DNA
- 2011
Linak, Margaret C.; Tourdot, Richard; Dorfman, Kevin D.
Linak, Margaret C.; Tourdot, Richard; Dorfman, Kevin D.
JOURNAL OF CHEMICAL PHYSICS 2011 Volume: 135
Article Number: 205102
Moving beyond Watson-Crick models of coarse
grained DNA dynamics
Wang, Qian; Liang, Kao-Chen; Czader,
Arkadiusz; et al.
PLOS COMPUTATIONAL BIOLOGY 2011 Volume: Article Number: e1002114
The Effect of Macromolecular Crowding, Ionic
Strength and Calcium Binding on Calmodulin Dynamics
Araque, Juan C.; Panagiotopoulos, Athanasios
Z.; Robert, Marc A.
JOURNAL OF CHEMICAL PHYSICS 2011 Volume: 134
Article Number: 165103
Lattice model of oligonucleotide hybridization
in solution. I. Model and thermodynamics
Ouldridge, Thomas E.; Louis, Ard A.; Doye,
Jonathan P. K.
JOURNAL OF CHEMICAL PHYSICS 2011 Volume: 134
Article Number: 085101
Structural, mechanical, and thermodynamic
properties of a coarse-grained DNA model
Leone, SR; Cremer, PS; Groves, JT; et al.
ANNUAL REVIEW OF PHYSICAL CHEMISTRY 2011 VOL
62 Book Series: Annual Review of
Physical Chemistry. Volume: 62 Pages:
555-574
Coarse-Grained Simulations of Macromolecules:
From DNA to Nanocomposites
Lillian, Todd D.; Perkins, N. C.
JOURNAL OF COMPUTATIONAL AND NONLINEAR
DYNAMICS 2011 Volume: 6 Article Number: 011008
Electrostatics and Self-Contact in an Elastic
Rod Approximation for DNA
Lara, Fernando Vargas; Starr, Francis W.
SOFT MATTER 2011 Volume: 7 Pages: 2085-2093
Stability of DNA-linked nanoparticle crystals
I: Effect of linker sequence and length
Beaber, Aaron; Gerberich, William
NATURE MATERIALS 2010 Volume: 9 Pages: 698-699
ALLOYS Strength from modelling
