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J. Pitera · SciRah

Researcher profile · Semantic Scholar

J. Pitera

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J. Pitera — researcher profile on SciRah

h-index: 34
Works: 86
Citations: 7,850

Most-cited papers

Development of an improved four-site water model for biomolecular simulations: TIP4P-Ew.
Hans W. Horn, William Swope, J. Pitera, J. Madura +3 more
2004Journal of Chemical Physics2,003 citations
Semantic Scholar
Extremely precise free energy calculations of amino acid side chain analogs: Comparison of common molecular mechanics force fields for proteins
M. Shirts, J. Pitera, William Swope, V. Pande
2003612 citations Open access
Semantic Scholar
Accelerating materials discovery using artificial intelligence, high performance computing and robotics
Edward O. Pyzer-Knapp, J. Pitera, P. Staar, Seiji Takeda +5 more
2022npj Computational Materials479 citations Open access
Semantic Scholar
Use of the Weighted Histogram Analysis Method for the Analysis of Simulated and Parallel Tempering Simulations.
J. Chodera, William Swope, J. Pitera, Chaok Seok +1 more
2007Journal of Chemical Theory and Computation454 citations Open access
Semantic Scholar
Describing Protein Folding Kinetics by Molecular Dynamics Simulations. 1. Theory
William Swope, J. Pitera, F. Suits
2004448 citations
Semantic Scholar
Understanding folding and design: Replica-exchange simulations of ``Trp-cage'' miniproteins
J. Pitera, William Swope
2003Proceedings of the National Academy of Sciences of the United States of America332 citations Open access
Semantic Scholar
Blue Gene: A vision for protein science using a petaflop supercomputer
F. Allen, G. Almási, W. Andreoni, D. Beece +48 more
2001IBM Systems Journal280 citations
Semantic Scholar
On the Use of Experimental Observations to Bias Simulated Ensembles.
J. Pitera, J. Chodera
2012Journal of Chemical Theory and Computation238 citations
Semantic Scholar
Long-Time Protein Folding Dynamics from Short-Time Molecular Dynamics Simulations
J. Chodera, William Swope, J. Pitera, K. Dill
2006Multiscale Modeling & simulation206 citations Open access
Semantic Scholar
Describing Protein Folding Kinetics by Molecular Dynamics Simulations. 2. Example Applications to Alanine Dipeptide and a β-Hairpin Peptide†
William Swope, J. Pitera, F. Suits, Michael Pitman +7 more
2004164 citations
Semantic Scholar
Dielectric properties of proteins from simulation: the effects of solvent, ligands, pH, and temperature.
J. Pitera, M. Falta, W. V. van Gunsteren
2001Biophysical Journal163 citations Open access
Semantic Scholar
Two-dimensional pattern formation using graphoepitaxy of PS-b-PMMA block copolymers for advanced FinFET device and circuit fabrication.
Hsinyu Tsai, J. Pitera, H. Miyazoe, S. Bangsaruntip +9 more
2014ACS Nano156 citations
Semantic Scholar
Heterogeneous folding of the trpzip hairpin: full atom simulation and experiment.
Wei-Yuan Yang, J. Pitera, William Swope, M. Gruebele
2004Journal of Molecular Biology149 citations
Semantic Scholar
Expected distributions of root-mean-square positional deviations in proteins.
J. Pitera
2014Journal of Physical Chemistry B144 citations
Semantic Scholar
Quantum-centric supercomputing for materials science: A perspective on challenges and future directions
Yuri Alexeev, Maximilian Amsler, Marco Antonio Barroca, Sanzio Bassini +124 more
2023Future generations computer systems134 citations Open access
Semantic Scholar
A Comparison of Non-Bonded Scaling Approaches for Free Energy Calculations
J. Pitera, W. V. van Gunsteren
2002125 citations
Semantic Scholar
Characterization of the TIP4P-Ew water model: vapor pressure and boiling point.
Hans W. Horn, William Swope, J. Pitera
2005Journal of Chemical Physics121 citations
Semantic Scholar
Simulations of the estrogen receptor ligand-binding domain: affinity of natural ligands and xenoestrogens.
B. Oostenbrink, J. Pitera, M. V. van Lipzig, J. H. Meerman +1 more
2000Journal of Medicinal Chemistry97 citations
Semantic Scholar
Broad-spectrum antimicrobial supramolecular assemblies with distinctive size and shape.
K. Fukushima, J. Tan, P. Korevaar, Yi-Yan Yang +15 more
2012ACS Nano88 citations Open access
Semantic Scholar
Supramolecular high-aspect ratio assemblies with strong antifungal activity
K. Fukushima, Shao-Qiong Liu, Hong Wu, Amanda C. Engler +11 more
2013Nature Communications84 citations Open access
Semantic Scholar
Soft patchy nanoparticles from solution-phase self-assembly of binary diblock copolymers.
G. Srinivas, J. Pitera
2008Nano letters (Print)81 citations Open access
Semantic Scholar
Blue Matter, an application framework for molecular simulation on Blue Gene
B. Fitch, R. Germain, M. Mendell, J. Pitera +8 more
2003J. Parallel Distributed Comput.64 citations
Semantic Scholar
Exhaustive mutagenesis in silico: Multicoordinate free energy calculations on proteins and peptides
J. Pitera, Peter A. Kollman
2000Proteins: Structure, Function, and Bioinformatics62 citations
Semantic Scholar
Determination of the internal morphology of nanostructures patterned by directed self assembly.
Daniel F. Sunday, M. Hammond, Cheng-Qing C. Wang, Wen-Li Wu +5 more
2014ACS Nano61 citations
Semantic Scholar
Biochemical characterization and crystallographic structure of an Escherichia coli protein from the phosphotriesterase gene family.
Jenny L. Buchbinder, R. Stephenson, M. Dresser, J. Pitera +2 more
1998Biochemistry61 citations Open access
Semantic Scholar
Blue Matter: Strong Scaling of Molecular Dynamics on Blue Gene/L
B. Fitch, A. Rayshubskiy, M. Eleftheriou, T. Ward +10 more
2006International Conference on Conceptual Structures60 citations
Semantic Scholar
Assessing the effect of conformational averaging on the measured values of observables
R. Bürgi, J. Pitera, W. V. van Gunsteren
2001Journal of Biomolecular NMR60 citations
Semantic Scholar
Enabling complex nanoscale pattern customization using directed self-assembly
G. Doerk, Joy Y. Cheng, Gurpreet Singh, C. Rettner +4 more
2014Nature Communications57 citations Open access
Semantic Scholar
One-Step Perturbation Methods for Solvation Free Energies of Polar Solutes
J. Pitera, W. V. van Gunsteren
200155 citations
Semantic Scholar
Multi-Label Patent Categorization with Non-Local Attention-Based Graph Convolutional Network
Pingjie Tang, Meng Jiang, Bryan (Ning) Xia, J. Pitera +2 more
2020AAAI Conference on Artificial Intelligence53 citations Open access
Semantic Scholar
The importance of solute-solvent van der Waals interactions with interior atoms of biopolymers.
J. Pitera, W. V. van Gunsteren
200153 citations
Semantic Scholar
Prediction of the binding free energies of new TIBO-like HIV-1 reverse transcriptase inhibitors using a combination of PROFEC, PB/SA, CMC/MD, and free energy calculations.
Mats A. L. Eriksson, J. Pitera, Peter A. Kollman
1999Journal of Medicinal Chemistry47 citations Open access
Semantic Scholar
Future Computing Hardware for AI
J. Welser, J. Pitera, C. Goldberg
2018International Electron Devices Meeting44 citations
Semantic Scholar
Absence of reptation in the high-temperature folding of the trpzip2 beta-hairpin peptide.
J. Pitera, I. Haque, William Swope
2006Journal of Chemical Physics44 citations
Semantic Scholar
Pattern placement accuracy in block copolymer directed self-assembly based on chemical epitaxy.
G. Doerk, Chi-Chun Liu, Joy Y. Cheng, C. Rettner +5 more
2013ACS Nano34 citations
Semantic Scholar
Comparison of computational approaches for predicting the effects of missense mutations on p53 function.
L. Chong, J. Pitera, William Swope, V. Pande
2009Journal of Molecular Graphics and Modelling34 citations
Semantic Scholar
Progress towards the integration of optical proximity correction and directed self-assembly of block copolymers with graphoepitaxy
Chi-Chun Liu, J. Pitera, N. Lafferty, K. Lai +4 more
2012Advanced Lithography30 citations
Semantic Scholar
Observation of noncooperative folding thermodynamics in simulations of 1BBL.
J. Pitera, William Swope, F. F. Abraham
2008Biophysical Journal30 citations Open access
Semantic Scholar
Molecular Inverse-Design Platform for Material Industries
Seiji Takeda, Toshiyuki Hama, Hsiang-Han Hsu, V. Piunova +16 more
2020Knowledge Discovery and Data Mining27 citations Open access
Semantic Scholar
Rapid directed self assembly of lamellar microdomains from a block copolymer containing hybrid
Joy Y. Cheng, J. Pitera, Oun-Ho Park, M. Flickner +3 more
200726 citations
Semantic Scholar
Designing an Optimum Guest for a Host Using Multimolecule Free Energy Calculations: Predicting the Best Ligand for Rebek's “Tennis Ball”
J. Pitera, P. Kollman
199825 citations
Semantic Scholar
Computational aspects of optical lithography extension by directed self-assembly
K. Lai, Chi-Chun Liu, J. Pitera, D. Dechene +11 more
2013Advanced Lithography24 citations
Semantic Scholar
Molecular Dynamics Simulation of Biomolecular Systems
W. van Gunsteren, D. Bakowies, R. Bürgi, I. Chandrasekhar +12 more
2001Chimia (Basel)24 citations Open access
Semantic Scholar
Orientation Control of Block Copolymers Using Surface Active, Phase-Preferential Additives.
Ankit Vora, K. Schmidt, Gabriela Alva, N. Arellano +7 more
2016ACS Applied Materials and Interfaces23 citations
Semantic Scholar
Directed Self-Assembly of Lamellar Microdomains of Block Copolymers Using Topographic Guiding Patterns
Sang-min Park, C. Rettner, J. Pitera, Ho-Cheol Kim
200921 citations
Semantic Scholar
The importance of solute-solvent van der Waals interactions with interior atoms of biopolymers.
J. Pitera, W. V. van Gunsteren
2001Journal of the American Chemical Society21 citations
Semantic Scholar
Correlation of early orientational ordering of engineered λ6–85 structure with kinetics and thermodynamics
E. Larios, J. Pitera, William Swope, M. Gruebele
200620 citations
Semantic Scholar
Blue Matter: Scaling of N-body simulations to one atom per node
B. Fitch, A. Rayshubskiy, M. Eleftheriou, T. Ward +5 more
2008IBM Journal of Research and Development19 citations
Semantic Scholar
Kinetic computational alanine scanning: application to p53 oligomerization.
L. Chong, William Swope, J. Pitera, V. Pande
2006Journal of Molecular Biology18 citations
Semantic Scholar
Reducing lambda repressor to the core.
Maxim B. Prigozhin, Krishnarjun Sarkar, Dennis Law, William Swope +2 more
2011Journal of Physical Chemistry B16 citations
Semantic Scholar

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