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1. Simulation Data for Design of Peptides that Fold and Self-Assemble on Graphite

   https://doi.org/10.5281/zenodo.6426152  

   Comer, Jeffrey ; Thakkar, Ravindra ; Velásquez-Silva, Astrid ; Miranda-Carvajal, Ingrid ( January 2022 )

   Abstract

   <p>This data set for the manuscript entitled &#34;Design of Peptides that Fold and Self-Assemble on Graphite&#34; 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.</p> <p>Version: 2.0</p> <p>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.</p> <p><br /> Conventions Used in These Files<br /> &#61;&#61;&#61;&#61;&#61;&#61;&#61;&#61;&#61;&#61;&#61;&#61;&#61;&#61;&#61;&#61;&#61;&#61;&#61;&#61;&#61;&#61;&#61;&#61;&#61;&#61;&#61;&#61;&#61;&#61;&#61;</p> <p>Structure Files<br /> ----------------<br /> - 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.)</p> <p>- graph_*.pdb or sol_*.pdb (initial coordinates before equilibration)<br /> - repart_*.psf (same as the above psf files, but the masses of non-water hydrogen atoms have been repartitioned by VMD script repartitionMass.tcl)<br /> - 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)<br /> - amber_*.prmtop (combined topology and parameter files for Amber force field simulations)<br /> - repart_amber_*.prmtop (same as the above prmtop files, but the masses of non-water hydrogen atoms have been repartitioned by ParmEd)</p> <p>Force Field Parameters<br /> ----------------------<br /> CHARMM format parameter files:<br /> - par_all36m_prot.prm (CHARMM36m FF for proteins)<br /> - 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.<br /> - toppar_water_ions_prot_cgenff.str (CHARMM water and ions with NBFIX parameters needed for protein and CGenFF included and others commented out)</p> <p>Template NAMD Configuration Files<br /> ---------------------------------<br /> These contain the most commonly used simulation parameters. They are called by the other NAMD configuration files (which are in the namd/ subdirectory):<br /> - template_min.namd (minimization)<br /> - template_eq.namd (NPT equilibration with lower graphene fixed)<br /> - template_abf.namd (for adaptive biasing force)</p> <p>Minimization<br /> -------------<br /> - namd/min_*.0.namd</p> <p>Equilibration<br /> -------------<br /> - namd/eq_*.0.namd</p> <p>Adaptive biasing force calculations<br /> -----------------------------------<br /> - namd/eabfZRest7_graph_chp1404.0.namd<br /> - namd/eabfZRest7_graph_chp1404.1.namd (continuation of eabfZRest7_graph_chp1404.0.namd)</p> <p>Log Files<br /> ---------<br /> 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.</p> <p>Simulation Output<br /> -----------------<br /> 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 &#61; 10 ns. The system cell trajectory is also included for the NPT runs are output/eq_*.xst.</p> <p>Scripts<br /> -------<br /> 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.</p> <p><br /> CONTENTS<br /> &#61;&#61;&#61;&#61;&#61;&#61;&#61;&#61;</p> <p>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.</p> <p>Sim_Figure-1: Simulations of N-acetylated C-amidated amino acids (Ac-X-NHMe) at the graphite–water interface.</p> <p>Sim_Figure-2: Simulations of different peptide designs (including acyclic, disulfide cyclized, and N-to-C cyclized) at the graphite–water interface.</p> <p>Sim_Figure-3: MM-GBSA calculations of different peptide sequences for a folded conformation and 5 misfolded/unfolded conformations.</p> <p>Sim_Figure-4: Simulation of four peptide molecules with the sequence cyc(GTGSGTG-GPGG-GCGTGTG-SGPG) at the graphite–water interface at 370 K.</p> <p>Sim_Figure-5: Simulation of four peptide molecules with the sequence cyc(GTGSGTG-GPGG-GCGTGTG-SGPG) at the graphite–water interface at 295 K.</p> <p>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.</p> <p>Sim_Figure-6: Simulation of the peptide molecule cyc(GTGSGTG-GPGG-GCGTGTG-SGPG) in free solution (no graphite).</p> <p>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 (&#34;doRestraintEnergyError.sh&#34;) 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.</p> <p>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.</p> <p>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.</p> <p>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.</p> <p>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.</p> <p> </p>
   

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   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.
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2. The benefit of Ca in improving pinning of BaZrO ₃ -Y ₂ O ₃ doubly-doped YBa ₂ Cu ₃ O _7-x /Ca _0.3 Y _0.7 Ba ₂ Cu ₃ O _7-x multilayer nanocomposite films

   https://doi.org/10.1088/2053-1591/acc7e3  

   Panth, Mohan ; Ogunjimi, Victor ; Sebastian, Mary Ann ; Gautam, Bibek ; Haugan, Timothy ; Wu, Judy ( April 2023 , Materials Research Express)

   Abstract This work examines the pinning enhancement in BaZrO 3 (BZO) +Y 2 O 3 doubly-doped (DD) YBa 2 Cu 3 O 7 (YBCO) nanocomposite multilayer (DD-ML) films. The film consists of two 10 nm thin Ca 0.3 Y 0.7 Ba 2 Cu 3 O 7-x (CaY-123) spacers stacking alternatively with three BZO + Y 2 O 3 /YBCO layers of 50 nm each in thickness that contain 3 vol% of Y 2 O 3 and BZO doping in the range of 2–6 vol%. Enhanced magnetic vortex pinning and improved pinning isotropy with respect to the orientation of magnetic field (B) have been achieved in the DD-ML samples at lower BZO doping as compared to that in the single-layer counterparts (DD-SL) without the CaY-123 spacers. For example, the pinning force density ( F p ) of ∼58 GNm −3 in 2 vol.% of DD-ML film is ∼110% higher than in 2 vol% of DD-SL at 65 K and B // c -axis, which is attributed to the improved pinning efficiency by c -axis aligned BZO nanorods through diffusion of Calcium (Ca) along the tensile-strained channels at BZO nanorods/YBCO interface for improvement of the interface microstructure and hence pinning efficiency ofmore »BZO nanorods. An additional benefit is in the considerably improved J c ( θ ) and reduced J c anisotropy in the former over the entire range of the B orientations. However, at higher BZO doping, the BZO nanorods become segmented and misoriented, which may change the Ca diffusion pathways and reduce the benefit of Ca in improving the pinning efficiency of BZO nanorods.« less
3. Synthesis, Elasticity, and Spin State of an Intermediate MgSiO ₃ ‐FeAlO ₃ Bridgmanite: Implications for Iron in Earth's Lower Mantle

   https://doi.org/10.1029/2020JB019964  

   Zhu, Feng ; Liu, Jiachao ; Lai, Xiaojing ; Xiao, Yuming ; Prakapenka, Vitali ; Bi, Wenli ; Alp, E. Ercan ; Dera, Przemyslaw ; Chen, Bin ; Li, Jie ( July 2020 , Journal of Geophysical Research: Solid Earth)

   Fe‐Al‐bearing bridgmanite may be the dominant host for ferric iron in Earth's lower mantle. Here we report the synthesis of (Mg_0.5Fe³⁺_0.5)(Al_0.5Si_0.5)O₃bridgmanite (FA50) with the highest Fe³⁺‐Al³⁺coupled substitution known to date. X‐ray diffraction measurements showed that at ambient conditions, the FA50 adopted the LiNbO₃structure. Upon compression at room temperature to 18 GPa, it transformed back into the bridgmanite structure, which remained stable up to 102 GPa and 2,600 K. Fitting Birch‐Murnaghan equation of state of FA50 bridgmanite yieldsV₀ = 172.1(4) ų,K₀ = 229(4) GPa withK₀′ = 4(fixed). The calculated bulk sound velocity of the FA50 bridgmanite is ~7.7% lower than MgSiO₃bridgmanite, mainly because the presence of ferric iron increases the unit‐cell mass by 15.5%. This difference likely represents the upper limit of sound velocity anomaly introduced by Fe³⁺‐Al³⁺substitution. X‐ray emission and synchrotron Mössbauer spectroscopy measurements showed that after laser annealing, ~6% of Fe³⁺cations exchanged with Al³⁺and underwent the high‐ to low‐spin transition at 59 GPa. The low‐spin proportion of Fe³⁺increased gradually with pressure and reached 17–31% at 80 GPa. Since the cation exchange and spin transition in this Fe³⁺‐Al³⁺‐enriched bridgmanite do not cause resolvable unit‐cell volume reduction, and the increase of low‐spin Fe³⁺fraction with pressure occurs gradually, the spin transition would not produce a distinct seismic signature in the lower mantle.more »However, it may influence iron partitioning and isotopic fractionation, thus introducing chemical heterogeneity in the lower mantle.

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4. Structural Behavior of C2/m Tremolite to 40 GPa: A High-Pressure Single-Crystal X-ray Diffraction Study

   https://doi.org/10.2138/am-2022-8278  

   Ott, Jason N. ; Kalkan, Bora ; Kunz, Martin ; Berlanga, Genesis ; Yuvali, Ali F. ; Williams, Quentin ( October 2022 , American Mineralogist)

   The high-pressure structure and stability of the calcic amphibole tremolite (Ca2Mg5Si8O22(OH)2) was investigated to ~40 GPa at 300 K by single-crystal X-ray diffraction using synchrotron radiation. C2/m symmetry tremolite displays a broader metastability range than previously studied clinoamphiboles, exhibiting no first-order phase transition up to 40 GPa. Axial parameter ratios a/b and a/c, in conjunction with finite strain versus normalized pressure trends, indicate that changes in compressional behavior occur at pressures of ~5 and ~20 GPa. An analysis of the finite strain trends, using third-order Birch-Murnaghan equations of state, resulted in bulk moduli (𝐾) of 72(7), 77(2), and 61(1) GPa for the compressional regimes from 0-5 GPa (regime I), 5-20 GPa (II), and above 20 GPa (III), respectively, and accompanying pressure-derivatives of the bulk moduli (𝐾′) of 8.6(42), 6.0(3), and 10.0(2). The results are consistent with first-principle theoretical calculations of tremolite elasticity. The axial compressibility ratios of tremolite, determined as 𝛽a : 𝛽b : 𝛽c = 2.22:1.0:0.78 (regime I), 2.12:1.0:0.96 (II), and 1.03:1.0:0.75 (III), demonstrate a substantial reduction of the compressional anisotropy of tremolite at high pressures, which is a notable contrast with the increasingly anisotropic compressibility observed in the high-pressure polymorphs of the clinoamphibole grunerite. The shift in compression-regimemore »at 5 GPa (I-II) transition is ascribed to stiffening along the crystallographic a-axis corresponding to closure of the vacant A-site in the structure, and a shift in the topology of the a-oriented surfaces of the structural I-beam from concave to convex. The II-III regime shift at 20 GPa corresponds to an increasing rate of compaction of the Ca-polyhedra and increased distortion of the Mg-octahedral sites, processes which dictate compaction in both high-pressure compression-regimes. Bond-valence analyses of the tremolite structure under pressure show dramatic overbonding of the Ca-cations (75% at 30 GPa), with significant Mg-cation overbonding as well (40%). These imply that tremolite’s notable metastability range hinges on the calcium cation’s bonding environment. The 8-fold coordinated Ca-polyhedron accommodates significant compaction under pressure, while the geometry of the Ca-O polyhedron becomes increasingly regular and inhibits the reorientation of the tetrahedral chains that generate phase transitions observed in other clinoamphiboles. Peak/background ratio of diffraction data collected above 40 GPa and our equation of state determination of bulk moduli and compressibilities of tremolite in regime III, in concert with the results of our previous Raman study, suggest that C2/m tremolite may be approaching the limit of its metastability above 40 GPa. Our results have relevance for both the metastable compaction of tremolite during impact events, and for possible metastable persistence of tremolite within cold subduction zones within the Earth.« less
5. Elucidating the Impact of Mg Substitution on the Properties of NASICON‐Na _{3+ y} V _{2− y} Mg _y (PO ₄ ) ₃ Cathodes

   https://doi.org/10.1002/adfm.202105463  

   Ghosh, Subham ; Barman, Nabadyuti ; Gonzalez‐Correa, Eliovardo ; Mazumder, Madhulika ; Zaveri, Aryan ; Giovine, Raynald ; Manche, Alexis ; Pati, Swapan K. ; Clément, Raphaële J. ; Senguttuvan, Premkumar ( August 2021 , Advanced Functional Materials)

   Vanadium multiredox‐based NASICON‐Na_zV_2−yM_y(PO₄)₃(3 ≤z ≤ 4; M = Al³⁺, Cr³⁺, and Mn²⁺) cathodes are particularly attractive for Na‐ion battery applications due to their high Na insertion voltage (>3.5 V vs Na⁺/Na⁰), reversible storage capacity (≈150 mA h g⁻¹), and rate performance. However, their practical application is hindered by rapid capacity fade due to bulk structural rearrangements at high potentials involving complex redox and local structural changes. To decouple these factors, a series of Mg²⁺‐substituted Na_3+yV_2−yMg_y(PO₄)₃(0 ≤y ≤ 1) cathodes is studied for which the only redox‐active species is vanadium. While X‐ray diffraction (XRD) confirms the formation of solid solutions between they = 0 and 1 end members, X‐ray absorption spectroscopy and solid‐state nuclear magnetic resonance reveal a complex evolution of the local structure upon progressive Mg²⁺substitution for V³⁺. Concurrently, the intercalation voltage rises from 3.35 to 3.45 V, due to increasingly more ionic VO bonds, and the sodium (de)intercalation mechanism transitions from a two‐phase fory ≤ 0.5 to a solid solution process fory ≥ 0.5, as confirmed by in operando XRD, while Na‐ion diffusion kinetics follow a nonlinear trend across the compositional series.