If you made any changes in Pure, your changes will be visible here soon.

Research Output 2007 2019

  • 1228 Citations
  • 15 h-Index
  • 22 Article
  • 1 Conference contribution
  • 1 Paper
  • 1 Review article
2019

An emergent understanding of strand displacement in RNA biology

Hong, F. & Sulc, P., Jan 1 2019, In : Journal of Structural Biology.

Research output: Contribution to journalArticle

RNA Folding
RNA
Nucleic Acid Conformation
DNA
Clustered Regularly Interspaced Short Palindromic Repeats

Triangulated Wireframe Structures Assembled Using Single-Stranded DNA Tiles

Matthies, M., Agarwal, N. P., Poppleton, E., Joshi, F. M., Sulc, P. & Schmidt, T. L., Jan 1 2019, (Accepted/In press) In : ACS Nano.

Research output: Contribution to journalArticle

Single-Stranded DNA
tiles
Tile
DNA
deoxyribonucleic acid
2018
2 Citations (Scopus)

Layered-Crossover Tiles with Precisely Tunable Angles for 2D and 3D DNA Crystal Engineering

Hong, F., Jiang, S., Lan, X., Narayanan, R. P., Sulc, P., Zhang, F., Liu, Y. & Yan, H., Nov 7 2018, In : Journal of the American Chemical Society. 140, 44, p. 14670-14676 7 p.

Research output: Contribution to journalArticle

Crystal engineering
Tile
DNA
Nanotechnology
Nanoparticles
7 Citations (Scopus)

Rapid Photoactuation of a DNA Nanostructure using an Internal Photocaged Trigger Strand

Liu, M., Jiang, S., Loza, O., Fahmi, N. E., Sulc, P. & Stephanopoulos, N., Jul 20 2018, In : Angewandte Chemie - International Edition. 57, 30, p. 9341-9345 5 p.

Research output: Contribution to journalArticle

Nanostructures
DNA
Bearings (structural)
Poly T
Poly A
2017
22 Citations (Scopus)

Self-assembling DNA nanotubes to connect molecular landmarks

Mohammed, A. M., Sulc, P., Zenk, J. & Schulman, R., May 1 2017, In : Nature Nanotechnology. 12, 4, p. 312-316 5 p.

Research output: Contribution to journalArticle

landmarks
assembling
Nanotubes
nanotubes
DNA
2016

Precision control of DNA-based molecular reactions

Ouldridge, T. E., Schreck, J. S., Romano, F., Sulc, P., Machinek, R. F., Haley, N. E. C., Louis, A. A., Doye, J. P. K., Bath, J. & Turberfield, A. J., Jan 1 2016.

Research output: Contribution to conferencePaper

DNA
2015
24 Citations (Scopus)

A comparison between parallelization approaches in molecular dynamics simulations on GPUs

Rovigatti, L., Sulc, P., Reguly, I. Z. & Romano, F., Oct 30 2015, In : Journal of Computational Chemistry. 36, 1, p. 1-8 8 p.

Research output: Contribution to journalArticle

Parallelization
Molecular Dynamics Simulation
Molecular dynamics
Graphics Processing Unit
Thread
4 Citations (Scopus)

Coarse-grained modelling of supercoiled RNA

Matek, C., Sulc, P., Randisi, F., Doye, J. P. K. & Louis, A. A., Dec 28 2015, In : Journal of Chemical Physics. 143, 24, 243122.

Research output: Contribution to journalArticle

RNA
Bubble formation
Denaturation
Double-Stranded RNA
biopolymer denaturation
22 Citations (Scopus)

DNA hairpins destabilize duplexes primarily by promoting melting rather than by inhibiting hybridization

Schreck, J. S., Ouldridge, T. E., Romano, F., Sulc, P., Shaw, L. P., Louis, A. A. & Doye, J. P. K., May 22 2015, In : Nucleic Acids Research. 43, 13, p. 6181-6190 10 p.

Research output: Contribution to journalArticle

Freezing
DNA
Base Pairing
Nanotechnology
Nucleotides
60 Citations (Scopus)

Introducing improved structural properties and salt dependence into a coarse-grained model of DNA

Snodin, B. E. K., Randisi, F., Mosayebi, M., Sulc, P., Schreck, J. S., Romano, F., Ouldridge, T. E., Tsukanov, R., Nir, E., Louis, A. A. & Doye, J. P. K., Jun 21 2015, In : Journal of Chemical Physics. 142, 23, 234901.

Research output: Contribution to journalArticle

Structural properties
deoxyribonucleic acid
Salts
salts
DNA
18 Citations (Scopus)

Modelling toehold-mediated RNA strand displacement

Sulc, P., Ouldridge, T. E., Romano, F., Doye, J. P. K. & Louis, A. A., Mar 10 2015, In : Biophysical Journal. 108, 5, p. 1238-1247 10 p.

Research output: Contribution to journalArticle

RNA
Nanotechnology
Temperature
Thermodynamics
Nucleic Acids
2014
38 Citations (Scopus)

A nucleotide-level coarse-grained model of RNA

Sulc, P., Romano, F., Ouldridge, T. E., Doye, J. P. K. & Louis, A. A., Jun 21 2014, In : Journal of Chemical Physics. 140, 23, 235102.

Research output: Contribution to journalArticle

nucleotides
Nucleotides
RNA
Nanorings
Double-Stranded RNA
91 Citations (Scopus)

Optimal distributed control of reactive power via the alternating direction method of multipliers

Sulc, P., Backhaus, S. & Chertkov, M., Dec 1 2014, In : IEEE Transactions on Energy Conversion. 29, 4, p. 968-977 10 p., 6963439.

Research output: Contribution to journalArticle

Reactive power
Networks (circuits)
Constrained optimization
Electric potential
Cost functions
16 Citations (Scopus)

Simulating a burnt-bridges DNA motor with a coarse-grained DNA model

Sulc, P., Ouldridge, T. E., Romano, F., Doye, J. P. K. & Louis, A. A., Jan 1 2014, In : Natural Computing. 13, 4, p. 535-547 13 p.

Research output: Contribution to journalArticle

Stators
DNA
Signal to noise ratio
Physics
2013
85 Citations (Scopus)

Coarse-graining DNA for simulations of DNA nanotechnology

Doye, J. P. K., Ouldridge, T. E., Louis, A. A., Romano, F., Sulc, P., Matek, C., Snodin, B. E. K., Rovigatti, L., Schreck, J. S., Harrison, R. M. & Smith, W. P. J., Dec 21 2013, In : Physical Chemistry Chemical Physics. 15, 47, p. 20395-20414 20 p.

Research output: Contribution to journalReview article

nanotechnology
Nanotechnology
deoxyribonucleic acid
DNA
simulation
86 Citations (Scopus)

DNA hybridization kinetics: Zippering, internal displacement and sequence dependence

Ouldridge, T. E., Sulc, P., Romano, F., Doye, J. P. K. & Louis, A. A., Oct 1 2013, In : Nucleic Acids Research. 41, 19, p. 8886-8895 10 p.

Research output: Contribution to journalArticle

Base Pairing
DNA
Nanotechnology
Thermodynamics
Temperature
157 Citations (Scopus)

On the biophysics and kinetics of toehold-mediated DNA strand displacement

Srinivas, N., Ouldridge, T. E., Sulc, P., Schaeffer, J. M., Yurke, B., Louis, A. A., Doye, J. P. K. & Winfree, E., Dec 1 2013, In : Nucleic Acids Research. 41, 22, p. 10641-10658 18 p.

Research output: Contribution to journalArticle

Biophysics
DNA
Thermodynamics
Base Pairing
Physical Phenomena
2012
2 Citations (Scopus)
Particle Tracking
kurtosis
Cage
Kurtosis
membranes
107 Citations (Scopus)

Sequence-dependent thermodynamics of a coarse-grained DNA model

Sulc, P., Romano, F., Ouldridge, T. E., Rovigatti, L., Doye, J. P. K. & Louis, A. A., Oct 7 2012, In : Journal of Chemical Physics. 137, 13, 135101.

Research output: Contribution to journalArticle

Melting point
deoxyribonucleic acid
melting
Thermodynamics
strands
2011
343 Citations (Scopus)

Options for control of reactive power by distributed photovoltaic generators

Turitsyn, K., Sulc, P., Backhaus, S. & Chertkov, M., Jun 1 2011, In : Proceedings of the IEEE. 99, 6, p. 1063-1073 11 p., 5768094.

Research output: Contribution to journalArticle

Reactive power
Voltage control
Networks (circuits)
Control systems
Distributed power generation
2010
11 Citations (Scopus)

Belief propagation for graph partitioning

Sulc, P. & Zdeborová, L., Jun 25 2010, In : Journal of Physics A: Mathematical and Theoretical. 43, 28, 285003.

Research output: Contribution to journalArticle

Graph Partitioning
Belief Propagation
Partitioning
Magnetization
Ising model
104 Citations (Scopus)

Distributed control of reactive power flow in a radial distribution circuit with high photovoltaic penetration

Turitsyn, K., Sulc, P., Backhaus, S. & Chertkov, M., Dec 6 2010, IEEE PES General Meeting, PES 2010. 5589663

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Reactive power
Networks (circuits)
Electric potential
Power generation
Electric power utilization
3 Citations (Scopus)

Quantifying slow evolutionary dynamics in RNA fitness landscapes

Sulc, P., Wagner, A. & Martin, O. C., Dec 1 2010, In : Journal of Bioinformatics and Computational Biology. 8, 6, p. 1027-1040 14 p.

Research output: Contribution to journalArticle

RNA
Genotype
Trajectories
3 Citations (Scopus)
Hitting Time
random walk
Random walk
Self-similarity
Graph in graph theory
2007
23 Citations (Scopus)

Group theoretical construction of mutually unbiased bases in Hilbert spaces of prime dimensions

Sulc, P. & Tolar, J., Dec 14 2007, In : Journal of Physics A: Mathematical and Theoretical. 40, 50, p. 15099-15111 13 p.

Research output: Contribution to journalArticle

Mutually Unbiased Bases
Hilbert spaces
Hilbert space
Unitary Operator
Heisenberg Group