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Physics

Biological Physics

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Displaying 76 - 100 of 197

Structural and Dynamical Order of a Disordered Protein: Molecular Insights into Conformational Switching of PAGE4 at the Systems Level

February 1, 2019
Author(s)
Xingcheng Ling, Prakash Kulkarni, Federico Bocci, Nicholas Schafer, Susmita Roy, Min-Yeh Tsai, Yanan He, Yihong Chen, Krithika Rajagopalan, Steven Mooney, Yu Zeng, Keith Weninger, Alexander Grishaev, Jose Onuchic, Herbert Levine, Peter Wolynes, Govindan Rangarajan, Vladimir Uversky, John Orban, Mohit Jolly
Folded proteins show a high degree of structural order and undergo (fairly constrained) collective motions related to their functions. On the other hand, intrinsically disordered proteins (IDPs), while lacking a well-defined three-dimensional structure, do

Mechanosensitive ion permeation across sub-nanoporous MoS2 monolayers

January 23, 2019
Author(s)
Alta Y. Fang, Kenneth Kroenlein, Alexander Smolyanitsky
We use all-atom molecular dynamics simulations informed by density functional theory calculations to investigate aqueous ion transport across subnanoporous monolayer molybdenum disulfide (MoS2) membranes subject to varying tensile strains. Driven by a

Highly mechanosensitive ion channels from graphene-embedded crown ethers

November 26, 2018
Author(s)
Alta Y. Fang, Kenneth Kroenlein, Demian Riccardi, Alexander Smolyanitsky
The ability to tune ionic permeation across nanoscale pores profoundly impacts diverse fields from nanofluidic computing to drug delivery. Here, we take advantage of complex formation between crown ethers and dissolved metal ions to demonstrate graphene

High-speed low-power neuromorphic systems based on magnetic Josephson junctions

October 25, 2018
Author(s)
Michael Schneider, Christine A. Donnelly, Stephen E. Russek
Josephson junctions and single flux quantum (SFQ) circuits form a natural neuromorphic technology with SFQ pulses and superconducting transmission lines simulating action potentials and axons, respectively. Josephson junctions consist of superconducting

Comment on "Innovative scattering analysis shows that hydrophobic disordered proteins are expanded in water"

August 30, 2018
Author(s)
Robert Best, Alessandro Borgia, Wenwei Zheng, Karin Buholzer, Madeleine Borgia, Hagen Hofmann, Daniel Nettels, Klaus Gast, Alexander Grishaev, Benjamin Schuler
The degree of compaction inferred from SAXS experiments by Riback et al. for unfolded proteins in water versus chemical denaturant is highly consistent with the results from FRET experiments. There is thus no "contradiction" between the two methods, nor

High-speed alignment optimization of digital optical phase conjugation systems based on autocovariance analysis in conjunction with orthonormal rectangular polynomials

August 28, 2018
Author(s)
Ashton S. Hemphill, Yuecheng Shen, Jeeseong C. Hwang, Lihong V. Wang
Digital optical phase conjugation (DOPC) enables many optical applications by permitting focusing of light through scattering media. However, DOPC systems require precise alignment of all optical components, particularly of the spatial light modulator (SLM

PAGE4 and Conformational Switching: Insights from Molecular Dynamics Simulations and Implications for Prostate Cancer

August 2, 2018
Author(s)
Alexander Grishaev, Xingcheng Lin, Mohit Jolly, Federico Bocci, Nicholas Schafer, Min-Yeh Tsai, Yihong Chen, Yanan He, Keith Weninger, John Orban, Prakash Kulkarni, Govindan Rangarajan, Herbert Levine, Jose Onuchic
Prostate-Associated Gene 4 (PAGE4) is a disordered protein implicated in the progression of prostate cancer. PAGE4 can be phosphorylated at two residue sites by Homeodomain-Interacting Protein Kinase 1 (HIPK1) to facilitate its binding to the Activator

A Spin-1 Representation for Dual-Funnel Energy Landscapes

July 20, 2018
Author(s)
Justin E. Elenewski, Kirill Velizhanin, Michael P. Zwolak
The interconversion between left- and right-handed helical folds of a polypeptide defines a dual-funneled free energy landscape. In this context, the funnel minima are connected through a continuum of unfolded conformations, evocative of the classical

Polyelectrolyte association and solvation

July 10, 2018
Author(s)
Alexandros Chremos, Jack F. Douglas
There has been significant interest in the tendency of highly charged particles having the same charge to form dynamic clusters in solution, but an accepted theoretical framework that can account for this ubiquitous phenomenon has been slow to develop. The

Golden aspect ratio for ion transport simulation in nanopores

July 5, 2018
Author(s)
Subin Sahu, Michael P. Zwolak
Access resistance indicates how well current carriers from the bulk medium can converge to a pore or opening, and is important in many fields, such as cell biology, electronics, electrochemical engineering, thermal transport, among others. In simplified

A trapped human PPM1A-phosphopeptide complex reveals structural features critical for regulation of PPM protein phosphatase activity

May 24, 2018
Author(s)
Subrata Debnath, Dalibor Kosek, Harichandra Tagad, Stewart R. Durell, Daniel Appella, Roderico Acevedo, Alexander Grishaev, Fred Dyda, Ettore Appella, Sharlyn Mazur
Metal-dependent protein phosphatases (PPM) are evolutionarily unrelated to other serine/threonine protein phosphatases and are characterized by their requirement for supplementation with millimolar concentrations of Mg2+ or Mn2+ ions for activity in vitro

Determining the physical properties of molecules with nanometer-scale pores

January 30, 2018
Author(s)
Haiyan Wang, Jessica Ettedgui, Jacob Fortater, Joseph W. Robertson, Joseph Reiner, Huisheng Zhang, Siping Chen, John J. Kasianowicz
Nanometer-scale pores have recently been developed for the detection, characterization, and quantitation of a wide range of analytes (e.g., ions, polymers, proteins, anthrax toxins, neurotransmitters, and synthetic nanoparticles), and for DNA sequencing

Maxwell-Hall access resistance in graphene nanopores

January 24, 2018
Author(s)
Subin Sahu, Michael P. Zwolak
The resistance due to the convergence from bulk to a constriction -- e.g., a nanopore -- is a mainstay of transport phenomena. In classical electrical conduction, Maxwell -- and later Hall for ionic conduction -- predicted this access or convergence

Zinc Doped Copper Ferrite Particles as Temperature Sensors for Magnetic Resonance Imaging

December 27, 2017
Author(s)
Karl Stupic, Janusz H. Hankiewicz, Zbigniew Celinski, Robert E. Camley, Marek Przybylski, Jan Zukrowski, Nick Anderson, Noweir Alghamdi, Nicholas Hammelev
We investigate the use of Cu0.35Zn0.65Fe2O4 particles as temperature-dependent sensors in magnetic resonance imaging (MRI). This material has a Curie temperature near 290 K, but in the large magnetic fields found in MRI scanners there is a significant

Hybrid Applications of Solution Scattering to Aid Structural Biology

November 19, 2017
Author(s)
Alexander Grishaev
Biomolecular applications of solution X-ray and neutron scattering (SAXS and SANS, respectively) started in late 1960s – early 1970s but were relatively limited in their ability to provide a detailed structural picture and lagged behind what became the two

Algorithm for rapid determination of optical scattering parameters

October 18, 2017
Author(s)
Zachary H. Levine, Adam L. Pintar, Richelle H. Streater, Anne-Michelle R. Lieberson, Catherine C. Cooksey, Paul Lemaillet
Preliminary experiments at the NIST Spectral Tri-function Automated Reference Reflectometer (STARR) facility have been conducted with the goal of providing the diffuse optical properties of a solid reference standard with optical properties similar to

Knot Energy, Complexity, and Mobility of Knotted Polymers

October 17, 2017
Author(s)
Luis F. Vargas Lara, Ahmed M. Hassan, Marc A. Mansfield, Jack F. Douglas
The Newtonian capacity C of an object is defined by the equilibrium energy, EN =1/C, of a charge distribution on a conductive object and provides a classical measure of object shape. It is well known, for example, that C is minimized for a sphere for all

Report for Dedicated JPSS VIIRS Ocean Color Calibration/Validation Cruise October 2016

October 2, 2017
Author(s)
Michael Ondrusek, Veronica P. Lance, Menghua Wang, Charles Kovach, Wesley Goode, Alex Gilerson, Sam Ahmed, Ahmed El-Habashi, Robert Foster, Matteo Ottaviani, Joaquim I. Goes, Helga de Rosario Gomes, Kali McKee, Joo Won Kang, Chuanmin Hu, Jennifer Cannizzaro, Shaojie Sun, David English, B. Carol Johnson, Zhongping Lee, Junfang Lin, Nicholas Tufillaro, Ivan Lalovic, Jasmine Nahorniak, Curtiss Davis, Mike Twardowski, Nicole Stockley, Kenneth Voss
The overall aim of the annual National Oceanic and Atmospheric Administration (NOAA) dedicated Joint Polar Satellite System (JPSS) Visible Infrared Imaging Radiometer Suite (VIIRS) ocean color calibration/validation (cal/val) cruises is to support

Consistent View of Polypeptide Chain Expansion in Chemical Denaturants from Multiple Experimental Methods

September 13, 2017
Author(s)
Alessandro Borgia, Wenwei Zheng, Karin Buholzer, Madeleine Borgia, Anja Schuler, Hagen Hoffman, Andrea Sorrano, Daniel Nettels, Klaus Gast, Alexander Grishaev, Robert Best, Benjamin Schuler
There has been a long-standing controversy regarding the effect of chemical denaturants on the dimensions of unfolded and intrinsically disordered proteins: A wide range of experimental techniques suggest that polypeptide chains expand with increasing

Non-Uniqueness in Dual-Energy CT with Beam Hardening

September 13, 2017
Author(s)
Zachary H. Levine
Purpose: The goal is to determine whether dual-energy computed tomography (CT) leads to a unique reconstruction into two basis materials. Methods and Materials: The beam hardening equation is simplified to the single voxel case. The simplified equation is
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