Search Results - "Pitera, Jed W"

On the Use of Experimental Observations to Bias Simulated Ensembles by Pitera, Jed W, Chodera, John D

“…Historically, experimental measurements have been used to bias biomolecular simulations toward structures compatible with those observations via the addition…”
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Accelerating materials discovery using artificial intelligence, high performance computing and robotics by Pyzer-Knapp, Edward O., Pitera, Jed W., Staar, Peter W. J., Takeda, Seiji, Laino, Teodoro, Sanders, Daniel P., Sexton, James, Smith, John R., Curioni, Alessandro

“…New tools enable new ways of working, and materials science is no exception. In materials discovery, traditional manual, serial, and human-intensive work is…”
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Understanding Folding and Design: Replica-Exchange Simulations of "Trp-Cage" Miniproteins by Pitera, Jed W., Swope, William

“…Replica-exchange molecular dynamics simulations in implicit solvent have been carried out to study the folding thermodynamics of a designed 20-residue peptide,…”
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Two-Dimensional Pattern Formation Using Graphoepitaxy of PS‑b‑PMMA Block Copolymers for Advanced FinFET Device and Circuit Fabrication by Tsai, Hsinyu, Pitera, Jed W, Miyazoe, Hiroyuki, Bangsaruntip, Sarunya, Engelmann, Sebastian U, Liu, Chi-Chun, Cheng, Joy Y, Bucchignano, James J, Klaus, David P, Joseph, Eric A, Sanders, Daniel P, Colburn, Matthew E, Guillorn, Michael A

“…Directed self-assembly (DSA) of lamellar phase block-co-polymers (BCPs) can be used to form nanoscale line-space patterns. However, exploiting the potential of…”
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Use of the Weighted Histogram Analysis Method for the Analysis of Simulated and Parallel Tempering Simulations by Chodera, John D, Swope, William C, Pitera, Jed W, Seok, Chaok, Dill, Ken A

“…The growing adoption of generalized-ensemble algorithms for biomolecular simulation has resulted in a resurgence in the use of the weighted histogram analysis…”
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Development of an improved four-site water model for biomolecular simulations: TIP4P-Ew by Horn, Hans W, Swope, William C, Pitera, Jed W, Madura, Jeffry D, Dick, Thomas J, Hura, Greg L, Head-Gordon, Teresa

“…A re-parameterization of the standard TIP4P water model for use with Ewald techniques is introduced, providing an overall global improvement in water…”
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Determination of the Internal Morphology of Nanostructures Patterned by Directed Self Assembly by Sunday, Daniel F, Hammond, Matthew R, Wang, Chengqing, Wu, Wen-li, Delongchamp, Dean M, Tjio, Melia, Cheng, Joy Y, Pitera, Jed W, Kline, R. Joseph

“…The directed self-assembly (DSA) of block copolymers (BCP) is an emerging resolution enhancement tool that can multiply or subdivide the pitch of a…”
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Expected Distributions of Root-Mean-Square Positional Deviations in Proteins by Pitera, Jed W

“…The atom positional root-mean-square deviation (RMSD) is a standard tool for comparing the similarity of two molecular structures. It is used to characterize…”
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Pattern Placement Accuracy in Block Copolymer Directed Self-Assembly Based on Chemical Epitaxy by Doerk, Gregory S, Liu, Chi-Chun, Cheng, Joy Y, Rettner, Charles T, Pitera, Jed W, Krupp, Leslie E, Topuria, Teya, Arellano, Noel, Sanders, Daniel P

“…The realization of viable designs for circuit patterns using the dense features formed by block copolymer directed self-assembly (DSA) will require a precise…”
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Heterogeneous Folding of the trpzip Hairpin: Full Atom Simulation and Experiment by Yang, Wei Yuan, Pitera, Jed W., Swope, William C., Gruebele, Martin

“…The β-hairpin trpzip2 can be tuned continuously from a two-state folder to folding on a rough energy landscape without a dominant refolding barrier. At high…”
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Dielectric Properties of Proteins from Simulation: The Effects of Solvent, Ligands, pH, and Temperature by Pitera, Jed W., Falta, Michael, van Gunsteren, Wilfred F.

“…We have used a standard Fröhlich-Kirkwood dipole moment fluctuation model to calculate the static dielectric permittivity, ϵ(0), for four different proteins,…”
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Directed Self-Assembly of Lamellar Microdomains of Block Copolymers Using Topographic Guiding Patterns by Park, Sang-Min, Rettner, Charles T, Pitera, Jed W, Kim, Ho-Cheol

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Interfacial Fluctuations of Block Copolymers:  A Coarse-Grain Molecular Dynamics Simulation Study by Srinivas, Goundla, Swope, William C, Pitera, Jed W

“…The lamellar and cylindrical phases of block copolymers have a number of technological applications, particularly when they occur in supported thin films. One…”
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Soft Patchy Nanoparticles from Solution-Phase Self-Assembly of Binary Diblock Copolymers by Srinivas, Goundla, Pitera, Jed W

“…The fabrication of highly ordered, defect-free nanostructures is a key challenge in nanotechnology. Bottom-up fabrication approaches require nanobuilding…”
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Enabling complex nanoscale pattern customization using directed self-assembly by Doerk, Gregory S., Cheng, Joy Y., Singh, Gurpreet, Rettner, Charles T., Pitera, Jed W., Balakrishnan, Srinivasan, Arellano, Noel, Sanders, Daniel P.

“…Block copolymer directed self-assembly is an attractive method to fabricate highly uniform nanoscale features for various technological applications, but the…”
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Simulations of the Estrogen Receptor Ligand-Binding Domain:  Affinity of Natural Ligands and Xenoestrogens by Oostenbrink, B. Chris, Pitera, Jed W, van Lipzig, Marola M. H, Meerman, John H. N, van Gunsteren, Wilfred F

“…We have carried out molecular dynamics (MD) simulations and free energy calculations on the α-subtype of the human estrogen receptor ligand-binding domain (ERα…”
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Describing Protein Folding Kinetics by Molecular Dynamics Simulations. 1. Theory by Swope, William C, Pitera, Jed W, Suits, Frank

“…A rigorous formalism for the extraction of state-to-state transition functions from a Boltzmann-weighted ensemble of microcanonical molecular dynamics…”
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Orientation Control of Block Copolymers Using Surface Active, Phase-Preferential Additives by Vora, Ankit, Schmidt, Kristin, Alva, Gabriela, Arellano, Noel, Magbitang, Teddie, Chunder, Anindarupa, Thompson, Leslie E, Lofano, Elizabeth, Pitera, Jed W, Cheng, Joy Y, Sanders, Daniel P

“…Orientation control of thin film nanostructures derived from block copolymers (BCPs) are of great interest for various emerging technologies like separation…”
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Describing Protein Folding Kinetics by Molecular Dynamics Simulations. 2. Example Applications to Alanine Dipeptide and a β-Hairpin Peptide by Swope, William C, Pitera, Jed W, Suits, Frank, Pitman, Mike, Eleftheriou, Maria, Fitch, Blake G, Germain, Robert S, Rayshubski, Aleksandr, Ward, T. J. C, Zhestkov, Yuriy, Zhou, Ruhong

“…In this work we demonstrate the use of a rigorous formalism for the extraction of state-to-state transition functions as a way to study the kinetics of protein…”
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Observation of Noncooperative Folding Thermodynamics in Simulations of 1BBL by Pitera, Jed W., Swope, William C., Abraham, Farid F.

“…One of the predictions of the energy landscape theory of protein folding is the possibility of barrierless, “downhill” folding under certain conditions. The…”
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