139 Publications (Page 1 of 6)
2020
Solution-Mediated Annealing Pathways Are Critical for Supramolecular Ordering of Complex Macrocycles at Surfaces
Castillo, Henry D⋅Castillo, Henry D⋅Castillo, Henry D.⋅Castillo, Henry D.⋅Yang, Jing⋅Yang, Jing⋅Yang, Jing⋅Yang, Jing⋅Debnath, Sibali⋅Debnath, Sibali⋅Debnath, Sibali⋅Debnath, Sibali⋅Dobscha, James R⋅Dobscha, James R⋅Dobscha, James R.⋅Dobscha, James R.⋅Trainor, Colleen Q.⋅Trainor, Colleen Q⋅Trainor, Colleen Q.⋅Trainor, Colleen Q⋅Mortensen, Riley D.⋅Mortensen, Riley D⋅Mortensen, Riley D⋅Mortensen, Riley D.⋅Raghavachari, Krishnan⋅Raghavachari, Krishnan⋅Raghavachari, Krishnan⋅Raghavachari, Krishnan⋅Flood, Amar H⋅Flood, Amar H.⋅Flood, Amar H⋅Flood, Amar H.⋅Ortoleva, Peter J.⋅Ortoleva, Peter J⋅Ortoleva, Peter J.⋅Ortoleva, Peter J⋅Tait, Steven L.⋅Tait, Steven L⋅Tait, Steven L. and Tait, Steven L
The Journal of Physical Chemistry C, vol. 124, (no. 12), pp. 6699, 2020-03-26. | Journal Article
 
Temporally Coarse-Grained All-Atom Molecular Dynamics Achieved via Stochastic Padé Approximants
Sereda, Yuriy V⋅Sereda, Yuriy V⋅Ortoleva, Peter J and Ortoleva, Peter J
The journal of physical chemistry. B, vol. 124, (no. 8), pp. 1410, 2020-Feb-27. | Journal Article
2019
Understanding the Origin of 2D Self-Assembly of Tricarbazole Macrocycles: An Integrated Quantum Mechanical/Molecular Dynamics Study
Debnath, Sibali⋅Debnath, Sibali⋅Yang, Jing⋅Yang, Jing⋅Ortoleva, Peter⋅Ortoleva, Peter⋅Raghavachari, Krishnan and Raghavachari, Krishnan
The Journal of Physical Chemistry C, vol. 123, (no. 28), pp. 17623, 2019-07-18. | Journal Article
2018
Amphiphile self-assembly dynamics at the solution-solid interface reveal asymmetry in head/tail desorption.
Castillo, Henry D⋅Castillo, Henry D⋅Espinosa-Duran, John M⋅Espinosa-Duran, John M⋅Dobscha, James R⋅Dobscha, James R⋅Ashley, Daniel C⋅Ashley, Daniel C⋅Debnath, Sibali⋅Debnath, Sibali⋅Hirsch, Brandon E⋅Hirsch, Brandon E⋅Schrecke, Samantha R⋅Schrecke, Samantha R⋅Baik, Mu-Hyun⋅Baik, Mu-Hyun⋅Ortoleva, Peter J⋅Ortoleva, Peter J⋅Raghavachari, Krishnan⋅Raghavachari, Krishnan⋅Flood, Amar H⋅Flood, Amar H⋅Tait, Steven L and Tait, Steven L
Chemical communications (Cambridge, England), August 7, 2018. | Journal Article
 
Multiscale Molecular Dynamics Approach to Energy Transfer in Nanomaterials
Espinosa-Duran, John M⋅Espinosa-Duran, John M⋅Sereda, Yuriy V⋅Sereda, Yuriy V⋅Abi-Mansour, Andrew⋅Abi-Mansour, Andrew⋅Ortoleva, Peter and Ortoleva, Peter
Journal of Chemical Theory and Computation, vol. 14, (no. 2), Feb 13, 2018. | Journal Article
2017
A multiscale molecular dynamics approach to energy transfer in nanomaterials
Espinosa-Duran, John Michael⋅Espinosa-Duran, John Michael⋅Sereda, Yuriy V⋅Sereda, Yuriy V⋅Abi-Mansour, Andrew⋅Abi-Mansour, Andrew⋅Ortoleva, Peter and Ortoleva, Peter
Journal of chemical theory and computation, 2017-Nov-30. | Journal Article
 
Multiscale time-dependent density functional theory: Demonstration for plasmons
Ortoleva, Peter J
The Journal of Chemical Physics, vol. 147, (no. 5), Aug 7, 2017. | Journal Article
2016
Implicit Time Integration for Multiscale Molecular Dynamics Using Transcendental Padé Approximants.
Abi Mansour, Andrew and Ortoleva, Peter J
Journal of chemical theory and computation, vol. 12, (no. 4), pp. 1965-1971, April 12, 2016. | Journal Article
 
Multiscale Modeling in the Clinic: Drug Design and Development
Clancy, C.E.⋅Clancy, Colleen⋅Clancy, Colleen E⋅Clancy, Colleen⋅Clancy, Colleen⋅Clancy, Colleen E⋅An, G.⋅An, Gary⋅An, Gary⋅An, Gary⋅An, Gary⋅An, Gary⋅Cannon, William R⋅Cannon, William R⋅Cannon, William⋅Cannon, William⋅Cannon, W.R.⋅Cannon, William⋅Liu, Yaling⋅Liu, Yaling⋅Liu, Yaling⋅Liu, Yaling⋅Liu, Yaling⋅Liu, Y.⋅May, Elebeoba E⋅May, Elebeoba⋅May, Elebeoba⋅May, Elebeoba E⋅May, Elebeoba⋅May, E.E.⋅Ortoleva, Peter⋅Ortoleva, Peter⋅Ortoleva, Peter⋅Ortoleva, Peter⋅Ortoleva, Peter⋅Ortoleva, P.⋅Popel, Aleksander⋅Popel, Aleksander S⋅Popel, Aleksander⋅Popel, Aleksander⋅Popel, Aleksander S⋅Popel, A.S.⋅Sluka, James⋅Sluka, James⋅Sluka, James⋅Sluka, J.P.⋅Sluka, James P⋅Sluka, James P⋅Su, J.⋅Su, Jing⋅Su, Jing⋅Su, Jing⋅Su, Jing⋅Su, Jing⋅Vicini, Paolo⋅Vicini, Paolo⋅Vicini, Paolo⋅Vicini, P.⋅Vicini, Paolo⋅Vicini, Paolo⋅Zhou, X.⋅Zhou, Xiaobo⋅Zhou, Xiaobo⋅Zhou, Xiaobo⋅Zhou, Xiaobo⋅Zhou, Xiaobo⋅Eckmann, David⋅Eckmann, David⋅Eckmann, David M⋅Eckmann, David M⋅Eckmann, D.M. and Eckmann, David
Annals of Biomedical Engineering, vol. 44, (no. 9), pp. 2610, 20160900. | Journal Article
 
ProtoMD: A prototyping toolkit for multiscale molecular dynamics
Somogyi, Endre⋅Mansour, Andrew Abi and Ortoleva, Peter J
Computer Physics Communications, vol. 202, pp. 350, May 2016. | Journal Article
 
Reverse Coarse-Graining for Equation-Free Modeling: Application to Multiscale Molecular Dynamics.
Abi Mansour, Andrew and Ortoleva, Peter J
Journal of chemical theory and computation, October 24, 2016. | Journal Article
2015
A Review of Two Multiscale Methods for the Simulation of Macromolecular Assemblies: Multiscale Perturbation and Multiscale Factorization
Pankavich, Stephen⋅Pankavich, Stephen⋅Ortoleva, Peter and Ortoleva, Peter
Computation, vol. 3, (no. 1), pp. 29-57, 2015. | Journal Article
 
Autonomous oscillation in supramolecular assemblies: Role of free energy landscape and fluctuations
Sereda, Yuriy V and Ortoleva, Peter J
Physica A: Statistical Mechanics and its Applications, vol. 437, pp. 456, 2015-11-01. | Journal Article
 
Broad spectrum assessment of the epitope fluctuation--Immunogenicity hypothesis.
Grosch, Jason S⋅Yang, Jing⋅Shen, Alice⋅Sereda, Yuriy V and Ortoleva, Peter J
Vaccine, vol. 33, (no. 44), pp. 5945-5949, November 4, 2015. | Journal Article
 
Early stage P22 viral capsid self-assembly mediated by scaffolding protein: atom-resolved model and molecular dynamics simulation.
Jiang, Jiajian⋅Jiang, Jiajian⋅Yang, Jing⋅Yang, Jing⋅Sereda, Yuriy V⋅Sereda, Yuriy V⋅Ortoleva, Peter J and Ortoleva, Peter J
The journal of physical chemistry. B, vol. 119, (no. 16), pp. 5156-5162, April 23, 2015. | Journal Article
 
Prospective on multiscale simulation of virus-like particles: Application to computer-aided vaccine design.
Abi Mansour, Andrew⋅Sereda, Yuriy V⋅Yang, Jing and Ortoleva, Peter J
Vaccine, vol. 33, (no. 44), pp. 5890-5896, November 4, 2015. | Journal Article
2014
A multiscale variational approach to the kinetics of viscous classical liquids: The coarse-grained mean field approximation.
Sereda, Yuriy V⋅Sereda, Yuriy V⋅Ortoleva, Peter J and Ortoleva, Peter J
The Journal of chemical physics, vol. 140, (no. 13), pp. 134104, 2014/Apr/7. | Journal Article
 
Energy transfer between a nanosystem and its host fluid: A multiscale factorization approach
Sereda, Yuriy V⋅Sereda, Yuriy V⋅Espinosa-Duran, John M⋅Espinosa-Duran, John M⋅Ortoleva, Peter J and Ortoleva, Peter J
The Journal of Chemical Physics, vol. 140, (no. 7), Feb 21, 2014. | Journal Article
 
Multiscale Factorization Method for Simulating Mesoscopic Systems with Atomic Precision.
Abi Mansour, Andrew and Ortoleva, Peter J
Journal of chemical theory and computation, vol. 10, (no. 2), pp. 518-523, February 11, 2014. | Journal Article
 
Nanosystem Self-Assembly Pathways Discovered via All-Atom Multiscale Analysis
Pankavich, Stephen⋅Pankavich, Stephen⋅Ortoleva, Peter and Ortoleva, Peter
2014-01-03. | Journal Article
2013
Epitope engineering and molecular metrics of immunogenicity: a computational approach to VLP-based vaccine design.
Joshi, Harshad⋅Joshi, Harshad⋅Lewis, Kristen⋅Lewis, Kristen⋅Singharoy, Abhishek⋅Singharoy, Abhishek⋅Ortoleva, Peter J and Ortoleva, Peter J
Vaccine, vol. 31, (no. 42), pp. 4841-7, 2013/Oct/1. | Journal Article
 
Epitope fluctuations in the human papillomavirus are under dynamic allosteric control: a computational evaluation of a new vaccine design strategy.
Singharoy, Abhishek⋅Polavarapu, Abhigna⋅Joshi, Harshad⋅Baik, Mu-Hyun and Ortoleva, Peter J
Journal of the American Chemical Society, vol. 135, (no. 49), pp. 18458-68, 2013/Dec/11. | Journal Article
 
Hierarchical Multiscale Modeling of Macromolecules and their Assemblies
Ortoleva, Peter⋅Ortoleva, Peter⋅Singharoy, Abhishek⋅Singharoy, Abhishek⋅Pankavich, Stephen and Pankavich, Stephen
2013-01-24. | Journal Article
 
ProtoMD: A Prototyping Toolkit for Multiscale Molecular Dynamics
Somogyi, Endre⋅Mansour, Andrew Abi and Ortoleva, Peter J
2013-09-25. | Journal Article
 
Reverse Coarse-graining for Equation-free Modeling: Application to Multiscale Molecular Dynamics
Mansour, Andrew Abi and Ortoleva, Peter J
2013-09-24. | Journal Article