Highly flexible multi-layered hydroxyapatite (HA) nanobelts were successfully grown and compared to nanorods. The nanomechanical behaviour of individual HA nanostructures was visualized using in situ TEM. Compression-induced deformation in HA nanobelts can spontaneously recover at a maximal strain of 99.2%, much larger than the 2.63% failure strain observed for traditional HA nanorods.
more »
« less
Brittle fracture to recoverable plasticity: polytypism-dependent nanomechanics in todorokite-like nanobelts
This paper shows polytypism dependent nanomechanics in todorokite-like nanobelts and reveals a plastic recovery regime in nanobelts with larger-width tunnel grains.
more » « less- NSF-PAR ID:
- 10075634
- Publisher / Repository:
- Royal Society of Chemistry (RSC)
- Date Published:
- Journal Name:
- Nanoscale Advances
- ISSN:
- 2516-0230
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
More Like this
-
-
more » « less
Abstract Rechargeable aqueous batteries with Zn2+as a working‐ion are promising candidates for grid‐scale energy storage because of their intrinsic safety, low‐cost, and high energy‐intensity. However, suitable cathode materials with excellent Zn2+‐storage cyclability must be found in order for Zinc‐ion batteries (ZIBs) to find practical applications. Herein, NaCa0.6V6O16·3H2O (NaCaVO) barnesite nanobelts are reported as an ultra‐stable ZIB cathode material. The original capacity reaches 347 mAh g−1at 0.1 A g−1, and the capacity retention rate is 94% after 2000 cycles at 2 A g−1and 83% after 10 000 cycles at 5 A g−1, respectively. Through a combined theoretical and experimental approach, it is discovered that the unique V3O8layered structure in NaCaVO is energetically favorable for Zn2+diffusion and the structural water situated between V3O8layers promotes a fast charge‐transfer and bulk migration of Zn2+by enlarging gallery spacing and providing more Zn‐ion storage sites. It is also found that Na+and Ca2+alternately suited in V3O8layers are the essential stabilizers for the layered structure, which play a crucial role in retaining long‐term cycling stability.
-
A capacitance increase phenomenon is observed for MoO 3 electrodes synthesized via a sol-gel process in the presence of dopamine hydrochloride (Dopa HCl) as compared to α-MoO 3 electrodes in 5M ZnCl 2 aqueous electrolyte. The synthesis approach is based on a hydrogen peroxide-initiated sol-gel reaction to which the Dopa HCl is added. The powder precursor (Dopa) x MoO y , is isolated from the metastable gel using freeze-drying. Hydrothermal treatment (HT) of the precursor results in the formation of MoO 3 accompanied by carbonization of the organic molecules; designated as HT-MoO 3 /C. HT of the precipitate formed in the absence of dopamine in the reaction produced α-MoO 3 , which was used as a reference material in this study (α-MoO 3 -ref). Scanning electron microscopy (SEM) images show a nanobelt morphology for both HT-MoO 3 /C and α-MoO 3 -ref powders, but with distinct differences in the shape of the nanobelts. The presence of carbonaceous content in the structure of HT-MoO 3 /C is confirmed by FTIR and Raman spectroscopy measurements. X-ray diffraction (XRD) and Rietveld refinement analysis demonstrate the presence of α-MoO 3 and h-MoO 3 phases in the structure of HT-MoO 3 /C. The increased specific capacitance delivered by the HT-MoO 3 /C electrode as compared to the α-MoO 3 -ref electrode in 5M ZnCl 2 electrolyte in a −0.25–0.70 V vs. Ag/AgCl potential window triggered a more detailed study in an expanded potential window. In the 5M ZnCl 2 electrolyte at a scan rate of 2 mV s −1 , the HT-MoO 3 /C electrode shows a second cycle capacitance of 347.6 F g −1 . The higher electrochemical performance of the HT-MoO 3 /C electrode can be attributed to the presence of carbon in its structure, which can facilitate electron transport. Our study provides a new route for further development of metal oxides for energy storage applications.more » « less
-
The past decade has witnessed the emergence of a new frontier in condensed matter physics: topological materials with an electronic band structure belonging to a different topological class from that of ordinary insulators and metals. This non-trivial band topology gives rise to robust, spin-polarized electronic states with linear energy–momentum dispersion at the edge or surface of the materials. For topological materials to be useful in electronic devices, precise control and accurate detection of the topological states must be achieved in nanostructures, which can enhance the topological states because of their large surface-to-volume ratios. In this Review, we discuss notable synthesis and electron transport results of topological nanomaterials, from topological insulator nanoribbons and plates to topological crystalline insulator nanowires and Weyl and Dirac semimetal nanobelts. We also survey superconductivity in topological nanowires, a nanostructure platform that might enable the controlled creation of Majorana bound states for robust quantum computations. Two material systems that can host Majorana bound states are compared: spin–orbit coupled semiconducting nanowires and topological insulating nanowires, a focus of this Review. Finally, we consider the materials and measurement challenges that must be overcome before topological nanomaterials can be used in next-generation electronic devices.more » « less
-
more » « less
This data set for the manuscript entitled "Design of Peptides that Fold and Self-Assemble on Graphite" includes all files needed to run and analyze the simulations described in the this manuscript in the molecular dynamics software NAMD, as well as the output of the simulations. The files are organized into directories corresponding to the figures of the main text and supporting information. They include molecular model structure files (NAMD psf or Amber prmtop format), force field parameter files (in CHARMM format), initial atomic coordinates (pdb format), NAMD configuration files, Colvars configuration files, NAMD log files, and NAMD output including restart files (in binary NAMD format) and trajectories in dcd format (downsampled to 10 ns per frame). Analysis is controlled by shell scripts (Bash-compatible) that call VMD Tcl scripts or python scripts. These scripts and their output are also included.
Version: 2.0
Changes versus version 1.0 are the addition of the free energy of folding, adsorption, and pairing calculations (Sim_Figure-7) and shifting of the figure numbers to accommodate this addition.
Conventions Used in These Files
===============================Structure Files
----------------
- graph_*.psf or sol_*.psf (original NAMD (XPLOR?) format psf file including atom details (type, charge, mass), as well as definitions of bonds, angles, dihedrals, and impropers for each dipeptide.)- graph_*.pdb or sol_*.pdb (initial coordinates before equilibration)
- repart_*.psf (same as the above psf files, but the masses of non-water hydrogen atoms have been repartitioned by VMD script repartitionMass.tcl)
- freeTop_*.pdb (same as the above pdb files, but the carbons of the lower graphene layer have been placed at a single z value and marked for restraints in NAMD)
- amber_*.prmtop (combined topology and parameter files for Amber force field simulations)
- repart_amber_*.prmtop (same as the above prmtop files, but the masses of non-water hydrogen atoms have been repartitioned by ParmEd)Force Field Parameters
----------------------
CHARMM format parameter files:
- par_all36m_prot.prm (CHARMM36m FF for proteins)
- par_all36_cgenff_no_nbfix.prm (CGenFF v4.4 for graphene) The NBFIX parameters are commented out since they are only needed for aromatic halogens and we use only the CG2R61 type for graphene.
- toppar_water_ions_prot_cgenff.str (CHARMM water and ions with NBFIX parameters needed for protein and CGenFF included and others commented out)Template NAMD Configuration Files
---------------------------------
These contain the most commonly used simulation parameters. They are called by the other NAMD configuration files (which are in the namd/ subdirectory):
- template_min.namd (minimization)
- template_eq.namd (NPT equilibration with lower graphene fixed)
- template_abf.namd (for adaptive biasing force)Minimization
-------------
- namd/min_*.0.namdEquilibration
-------------
- namd/eq_*.0.namdAdaptive biasing force calculations
-----------------------------------
- namd/eabfZRest7_graph_chp1404.0.namd
- namd/eabfZRest7_graph_chp1404.1.namd (continuation of eabfZRest7_graph_chp1404.0.namd)Log Files
---------
For each NAMD configuration file given in the last two sections, there is a log file with the same prefix, which gives the text output of NAMD. For instance, the output of namd/eabfZRest7_graph_chp1404.0.namd is eabfZRest7_graph_chp1404.0.log.Simulation Output
-----------------
The simulation output files (which match the names of the NAMD configuration files) are in the output/ directory. Files with the extensions .coor, .vel, and .xsc are coordinates in NAMD binary format, velocities in NAMD binary format, and extended system information (including cell size) in text format. Files with the extension .dcd give the trajectory of the atomic coorinates over time (and also include system cell information). Due to storage limitations, large DCD files have been omitted or replaced with new DCD files having the prefix stride50_ including only every 50 frames. The time between frames in these files is 50 * 50000 steps/frame * 4 fs/step = 10 ns. The system cell trajectory is also included for the NPT runs are output/eq_*.xst.Scripts
-------
Files with the .sh extension can be found throughout. These usually provide the highest level control for submission of simulations and analysis. Look to these as a guide to what is happening. If there are scripts with step1_*.sh and step2_*.sh, they are intended to be run in order, with step1_*.sh first.
CONTENTS
========The directory contents are as follows. The directories Sim_Figure-1 and Sim_Figure-8 include README.txt files that describe the files and naming conventions used throughout this data set.
Sim_Figure-1: Simulations of N-acetylated C-amidated amino acids (Ac-X-NHMe) at the graphite–water interface.
Sim_Figure-2: Simulations of different peptide designs (including acyclic, disulfide cyclized, and N-to-C cyclized) at the graphite–water interface.
Sim_Figure-3: MM-GBSA calculations of different peptide sequences for a folded conformation and 5 misfolded/unfolded conformations.
Sim_Figure-4: Simulation of four peptide molecules with the sequence cyc(GTGSGTG-GPGG-GCGTGTG-SGPG) at the graphite–water interface at 370 K.
Sim_Figure-5: Simulation of four peptide molecules with the sequence cyc(GTGSGTG-GPGG-GCGTGTG-SGPG) at the graphite–water interface at 295 K.
Sim_Figure-5_replica: Temperature replica exchange molecular dynamics simulations for the peptide cyc(GTGSGTG-GPGG-GCGTGTG-SGPG) with 20 replicas for temperatures from 295 to 454 K.
Sim_Figure-6: Simulation of the peptide molecule cyc(GTGSGTG-GPGG-GCGTGTG-SGPG) in free solution (no graphite).
Sim_Figure-7: Free energy calculations for folding, adsorption, and pairing for the peptide CHP1404 (sequence: cyc(GTGSGTG-GPGG-GCGTGTG-SGPG)). For folding, we calculate the PMF as function of RMSD by replica-exchange umbrella sampling (in the subdirectory Folding_CHP1404_Graphene/). We make the same calculation in solution, which required 3 seperate replica-exchange umbrella sampling calculations (in the subdirectory Folding_CHP1404_Solution/). Both PMF of RMSD calculations for the scrambled peptide are in Folding_scram1404/. For adsorption, calculation of the PMF for the orientational restraints and the calculation of the PMF along z (the distance between the graphene sheet and the center of mass of the peptide) are in Adsorption_CHP1404/ and Adsorption_scram1404/. The actual calculation of the free energy is done by a shell script ("doRestraintEnergyError.sh") in the 1_free_energy/ subsubdirectory. Processing of the PMFs must be done first in the 0_pmf/ subsubdirectory. Finally, files for free energy calculations of pair formation for CHP1404 are found in the Pair/ subdirectory.
Sim_Figure-8: Simulation of four peptide molecules with the sequence cyc(GTGSGTG-GPGG-GCGTGTG-SGPG) where the peptides are far above the graphene–water interface in the initial configuration.
Sim_Figure-9: Two replicates of a simulation of nine peptide molecules with the sequence cyc(GTGSGTG-GPGG-GCGTGTG-SGPG) at the graphite–water interface at 370 K.
Sim_Figure-9_scrambled: Two replicates of a simulation of nine peptide molecules with the control sequence cyc(GGTPTTGGGGGGSGGPSGTGGC) at the graphite–water interface at 370 K.
Sim_Figure-10: Adaptive biasing for calculation of the free energy of the folded peptide as a function of the angle between its long axis and the zigzag directions of the underlying graphene sheet.
This material is based upon work supported by the US National Science Foundation under grant no. DMR-1945589. A majority of the computing for this project was performed on the Beocat Research Cluster at Kansas State University, which is funded in part by NSF grants CHE-1726332, CNS-1006860, EPS-1006860, and EPS-0919443. This work used the Extreme Science and Engineering Discovery Environment (XSEDE), which is supported by National Science Foundation grant number ACI-1548562, through allocation BIO200030.
