J. Pitera

发表

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, 2004 .

Current developments in and importance of high-performance computing in drug discovery.

J. Pitera, 2009, Current opinion in drug discovery & development.

Blue Gene: A vision for protein science using a petaflop supercomputer

Ajay K. Royyuru, José E. Moreira, Alessandro Curioni, 2001, IBM Syst. J..

Heterogeneous folding of the trpzip hairpin: full atom simulation and experiment.

M. Gruebele, William Swope, J. Pitera, 2004, Journal of molecular biology.

Fundamental study of extreme UV resist line edge roughness: Characterization, experiment, and modeling

K. Virwani, G. Wallraff, W. Hinsberg, 2012 .

Development of an improved four-site water model for biomolecular simulations: TIP4P-Ew.

Greg L. Hura, Hans W. Horn, J. Madura, 2004, The Journal of chemical physics.

Two-dimensional pattern formation using graphoepitaxy of PS-b-PMMA block copolymers for advanced FinFET device and circuit fabrication.

Chi-Chun Liu, Hsinyu Tsai, Sarunya Bangsaruntip, 2014, ACS nano.

Broad-spectrum antimicrobial supramolecular assemblies with distinctive size and shape.

E. W. Meijer, Amanda C. Engler, Yi Yan Yang, 2012, ACS nano.

Accelerating materials discovery using artificial intelligence, high performance computing and robotics

Edward O. Pyzer-Knapp, Daniel P. Sanders, T. Laino, 2022, npj Computational Materials.

Dielectric properties of proteins from simulation: the effects of solvent, ligands, pH, and temperature.

J. Pitera, W. V. van Gunsteren, W. V. Gunsteren, 2001, Biophysical journal.

Understanding folding and design: Replica-exchange simulations of ``Trp-cage'' miniproteins

William Swope, J. Pitera, 2003, Proceedings of the National Academy of Sciences of the United States of America.

Determination of the internal morphology of nanostructures patterned by directed self assembly.

Joy Y. Cheng, R. J. Kline, J. Pitera, 2014, ACS nano.

Rapid directed self assembly of lamellar microdomains from a block copolymer containing hybrid

Joy Y. Cheng, M. Flickner, Ho-Cheol Kim, 2007 .

Directed Self-Assembly of Lamellar Microdomains of Block Copolymers Using Topographic Guiding Patterns

C. Rettner, Ho-Cheol Kim, Sang-Min Park, 2009 .

Assessing the effect of conformational averaging on the measured values of observables

J. Pitera, W. V. van Gunsteren, R. Bürgi, 2001, Journal of biomolecular NMR.

Describing Protein Folding Kinetics by Molecular Dynamics Simulations. 1. Theory

William Swope, J. Pitera, F. Suits, 2004 .

Extremely precise free energy calculations of amino acid side chain analogs: Comparison of common molecular mechanics force fields for proteins

Michael R. Shirts, M. Shirts, V. Pande, 2003 .

Interfacial fluctuations of block copolymers: a coarse-grain molecular dynamics simulation study.

William Swope, J. Pitera, G. Srinivas, 2007, The journal of physical chemistry. B.

Graphical visualization of mean hydration from molecular dynamics simulations.

P. Kollman, J. Pitera, 1997, Journal of Molecular Graphics and Modelling.

Soft patchy nanoparticles from solution-phase self-assembly of binary diblock copolymers.

J. Pitera, G. Srinivas, 2008, Nano letters.

Erratum: Biochemical characterization and crystallographic structure of an Escherichia coli protein from the phosphotriesterase gene family (Biochemistry (April 14, 1998) 37:15 (5096-5106))

R. Fletterick, J. Pitera, T. Scanlan, 1998 .

Chapter 6 Blue Matter: Scaling of N-Body Simulations to One Atom per Node

Robert S. Germain, Blake G. Fitch, Aleksandr Rayshubskiy, 2008 .

Supramolecular high-aspect ratio assemblies with strong antifungal activity

Amanda C. Engler, Yi Yan Yang, J. Hedrick, 2013, Nature Communications.

Expected distributions of root-mean-square positional deviations in proteins.

J. Pitera, 2014, The journal of physical chemistry. B.

Self-assembly in casting solutions of block copolymer membranes

V. Calo, J. Pitera, S. Nunes, 2013 .

Absence of reptation in the high-temperature folding of the trpzip2 beta-hairpin peptide.

William C Swope, Jed W Pitera, William Swope, 2006, The Journal of chemical physics.

Use of the Weighted Histogram Analysis Method for the Analysis of Simulated and Parallel Tempering Simulations.

Ken A Dill, John D Chodera, William C Swope, 2007, Journal of chemical theory and computation.

Essential Step Toward Mining Big Polymer Data: PolyName2Structure, Mapping Polymer Names to Structures

Yufeng J. Tseng, Pei-Hua Wang, Daniel P. Sanders, 2020 .

Blue Matter: Scaling of N-body simulations to one atom per node

Robert S. Germain, Mark Giampapa, Blake G. Fitch, 2008, IBM J. Res. Dev..

Parallel implementation of the replica exchange molecular dynamics algorithm on Blue Gene/L

Robert S. Germain, Ruhong Zhou, Blake G. Fitch, 2006, Proceedings 20th IEEE International Parallel & Distributed Processing Symposium.

On the Use of Experimental Observations to Bias Simulated Ensembles.

John D Chodera, Jed W Pitera, J. Chodera, 2012, Journal of chemical theory and computation.

Exhaustive mutagenesis in silico: Multicoordinate free energy calculations on proteins and peptides

P. Kollman, J. Pitera, 2000, Proteins.

Long-Time Protein Folding Dynamics from Short-Time Molecular Dynamics Simulations

John D. Chodera, Ken A. Dill, Jed W. Pitera, 2006, Multiscale Model. Simul..

Observation of noncooperative folding thermodynamics in simulations of 1BBL.

William Swope, J. Pitera, F. Abraham, 2008, Biophysical journal.

Characterization of the TIP4P-Ew water model: vapor pressure and boiling point.

Hans W. Horn, William C Swope, Jed W Pitera, 2005, The Journal of chemical physics.

Designing an Optimum Guest for a Host Using Multimolecule Free Energy Calculations: Predicting the Best Ligand for Rebek's “Tennis Ball”

Peter A. Kollman, Jed Pitera, P. Kollman, 1998 .

The importance of solute-solvent van der Waals interactions with interior atoms of biopolymers.

W F van Gunsteren, J. Pitera, W. V. van Gunsteren, 2001, Journal of the American Chemical Society.

Enabling complex nanoscale pattern customization using directed self-assembly

Charles T. Rettner, Daniel P. Sanders, Gurpreet Singh, 2014, Nature Communications.

Block Copolymer Thin Films on Patterned Substrates

J. Pitera, J. Cheng, Hc-C. Kim, 2012 .

Biochemical characterization and crystallographic structure of an Escherichia coli protein from the phosphotriesterase gene family.

R J Fletterick, R. Fletterick, J. Pitera, 1998, Biochemistry.

Future Computing Hardware for AI

J. Welser, J. W. Pitera, C. Goldberg, 2018, 2018 IEEE International Electron Devices Meeting (IEDM).

Kinetic computational alanine scanning: application to p53 oligomerization.

Vijay S Pande, William C Swope, Jed W Pitera, 2006, Journal of molecular biology.

Comparison of computational approaches for predicting the effects of missense mutations on p53 function.

Vijay S Pande, William C Swope, Jed W Pitera, 2009, Journal of molecular graphics & modelling.

Multi-Label Patent Categorization with Non-Local Attention-Based Graph Convolutional Network

Nitesh V. Chawla, Bryan Xia, Meng Jiang, 2020, AAAI.

Molecular Inverse-Design Platform for Material Industries

Daiju Nakano, Shuichi Hirose, Hiroki Toda, 2020, KDD.

Orientation Control of Block Copolymers Using Surface Active, Phase-Preferential Additives.

Joy Y. Cheng, Elizabeth M. Lofano, J. Pitera, 2016, ACS applied materials & interfaces.

Strategies to enable directed self-assembly contact hole shrink for tight pitches

Nelson Felix, Martha I. Sanchez, Cheng Chi, 2016, SPIE Advanced Lithography.

Computational aspects of optical lithography extension by directed self-assembly

Neal Lafferty, Joy Cheng, Hsinyu Tsai, 2013, Advanced Lithography.

Pattern placement accuracy in block copolymer directed self-assembly based on chemical epitaxy.

Chi-Chun Liu, Teya Topuria, Noel Arellano, 2013, ACS nano.

Measurement of placement error between self-assembled polymer patterns and guiding chemical prepatterns

Chi-Chun Liu, Charles T. Rettner, Daniel P. Sanders, 2012, Advanced Lithography.

Blue Matter: Strong Scaling of Molecular Dynamics on Blue Gene/L

Robert S. Germain, Mark Giampapa, Ruhong Zhou, 2006, International Conference on Computational Science.

DSA via hole shrink for advanced node applications

Nelson Felix, Kafai Lai, Martha I. Sanchez, 2016, SPIE Advanced Lithography.

Blue Matter, an application framework for molecular simulation on Blue Gene

Robert S. Germain, Ruhong Zhou, Blake G. Fitch, 2003, J. Parallel Distributed Comput..

Materials Science Literature-Patent Relevance Search: A Heterogeneous Network Analysis Approach

Nitesh V. Chawla, Pingjie Tang, Dmitry Zubarev, 2017, 2017 IEEE International Conference on Data Science and Advanced Analytics (DSAA).

A Comparison of Non-Bonded Scaling Approaches for Free Energy Calculations

Jed W. Pitera, Wilfred F. van Gunsteren, J. Pitera, 2002 .

Overview of molecular dynamics techniques and early scientific results from the Blue Gene project

Robert S. Germain, Michael Pitman, Frank Suits, 2005, IBM J. Res. Dev..

One-Step Perturbation Methods for Solvation Free Energies of Polar Solutes

Wilfred F. van Gunsteren, Jed W. Pitera, J. Pitera, 2001 .

Cognitive Materials Discovery and Onset of the 5th Discovery Paradigm

J. Pitera, D. Zubarev, 2019, ACS Symposium Series.

AI-driven Inverse Design System for Organic Molecules pdf

Toshiyuki Yamane, Daiju Nakano, Daniel P. Sanders, 2020, ArXiv.

Programmable nanoparticle ensembles via high-throughput directed self-assembly.

Joy Y. Cheng, C. Rettner, J. Pitera, 2013, Langmuir : the ACS journal of surfaces and colloids.

Simulations of the estrogen receptor ligand-binding domain: affinity of natural ligands and xenoestrogens.

J. Pitera, W. V. van Gunsteren, J. Meerman, 2000, Journal of medicinal chemistry.

Molecular Dynamics Simulation of Biomolecular Systems

Chris Oostenbrink, Xavier Daura, Christine Peter, 2001, CHIMIA.

Two-dimensional pattern formation using graphoepitaxy of PS-b-PMMA block copolymers for advanced FinFET device and circuit fabrication.

Joy Y. Cheng, E. Joseph, J. Pitera, 2014, ACS nano.

Design technology co-optimization assessment for directed self-assembly-based lithography: design for directed self-assembly or directed self-assembly for design?

Nelson Felix, Markus Brink, Chi-Chun Liu, 2017 .

Quantum-centric supercomputing for materials science: A perspective on challenges and future directions

Gokul Subramanian Ravi, Jennifer R. Glick, Douglas M. Jennewein, 2024, Future Generation Computer Systems.

Molecule Generation Experience: An Open Platform of Material Design for Public Users pdf

Daiju Nakano, Akihiro Kishimoto, Toshiyuki Hama, 2021, ArXiv.