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1. Searching for correlations between vibrational spectral features and structural parameters of silicate glass network

   https://doi.org/10.1111/jace.17036  

   Liu, Hongshen ; Hahn, Seung Ho ; Ren, Mengguo ; Thiruvillamalai, Mahadevan ; Gross, Timothy M. ; Du, Jincheng ; van Duin, Adri C. T. ; Kim, Seong H. ( February 2020 , Journal of the American Ceramic Society)

   Infrared (IR) and Raman spectroscopic features of silicate glasses are often interpreted based on the analogy with those of smaller molecules, molecular clusters, or crystalline counterparts; this study tests the accuracy and validity of these widely cited peak assignment schemes by comparing vibrational spectral features with bond parameters of the glass network created by molecular dynamics (MD) simulations. A series of sodium silicate glasses with compositions of [Na₂O]_x[Al₂O₃]₂[SiO₂]_98−xwithx = 7, 12, 17, and 22 were synthesized and analyzed with IR and Raman. A silica glass substrate and a crystalline quartz were also analyzed for comparison. Glass structures with the same compositions were generated with MD simulations using three types of potentials: fixed partial charge pairwise (Teter), partial diffuse charge potential (MGFF), and bond order‐based charge transfer potential (ReaxFF). The comparison of simulated and experimental IR spectra showed that, among these three potentials tested, ReaxFF reproduces the concentration dependence of spectral features closest to the experimentally observed trend. Thus, the bond length and angle distributions as well as Si–Qⁿspecies and ring size distributions of silica and sodium silicate glasses were obtained from ReaxFF‐MD simulations and further compared with the peak assignment or deconvolution schemes—which have been widely used since 1970s and 1980s—(a) correlation between the IR peak position in the Si–O stretch region (1050‐1120 cm⁻¹) and the Si–O–Si bond angle; (b) deconvolution of the Raman bands in the Si–O stretch region with theQⁿspeciation; and (c) assignment of the Raman bands in the 420‐600 cm⁻¹region to the bending modes of (SiO)_nrings with different sizes (typically, n = 3‐6). The comparisons showed that none of these widely used methods is congruent with the bond parameters or structures of silicate glass networks produced via ReaxFF‐MD simulations. This finding invokes that the adequacy of these spectral interpretation methods must be questioned. Alternative interpretations are proposed, which are to be tested independently in future studies.

    

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2. 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 , Zenodo)

   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.namd

   Equilibration
   -------------
   - namd/eq_*.0.namd

   Adaptive 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. 

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3. Modeling the effects of lattice defects on microtubule breaking and healing

   https://doi.org/10.1002/cm.21346  

   Jiang, Nan ; Bailey, Megan E. ; Burke, Jessica ; Ross, Jennifer L. ; Dima, Ruxandra I. ( January 2017 , Cytoskeleton)

   Microtubule reorganization often results from the loss of polymer induced through breakage or active destruction by energy‐using enzymes. Pre‐existing defects in the microtubule lattice likely lower structural integrity and aid filament destruction. Using large‐scale molecular simulations, we model diverse microtubule fragments under forces generated at specific positions to locally crush the filament. We show that lattices with 2% defects are crushed and severed by forces three times smaller than defect‐free ones. We validate our results with direct comparisons of microtubule kinking angles during severing. We find a high statistical correlation between the angle distributions from experiments and simulations indicating that they sample the same population of structures. Our simulations also indicate that the mechanical environment of the filament affects breaking: local mechanical support inhibits healing after severing, especially in the case of filaments with defects. These results recall reports of microtubule healing after flow‐induced bending and corroborate prior experimental studies that show severing is more likely at locations where microtubules crossover in networks. Our results shed new light on mechanisms underlying the ability of microtubules to be destroyed and healed in the cell, either by external forces or by severing enzymes wedging dimers apart. © 2016 Wiley Periodicals, Inc.

    

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4. Role of tilt grain boundaries on the structural integrity of WSe 2 monolayers

   https://doi.org/10.1039/D2CP03492A  

   Sakib, Nuruzzaman ; Paul, Shiddartha ; Nayir, Nadire ; van Duin, Adri C. ; Neshani, Sara ; Momeni, Kasra ( November 2022 , Physical Chemistry Chemical Physics)

   Transition metal dichalcogenides (TMDCs) are potential materials for future optoelectronic devices. Grain boundaries (GBs) can significantly influence the optoelectronic properties of TMDC materials. Here, we have investigated the mechanical characteristics of tungsten diselenide (WSe 2 ) monolayers and failure process with symmetric tilt GBs using ReaxFF molecular dynamics simulations. In particular, the effects of topological defects, loading rates, and temperatures are investigated. We considered nine different grain boundary structures of monolayer WSe 2 , of which six are armchair (AC) tilt structures, and the remaining three are zigzag (ZZ) tilt structures. Our results indicate that both tensile strength and fracture strain of WSe 2 with symmetric tilt GBs decrease as the temperature increases. We revealed an interfacial phase transition for high-angle GBs reduces the elastic strain energy within the interface at finite temperatures. Furthermore, brittle cracking is the dominant failure mode in the WSe 2 monolayer with tilted GBs. WSe 2 GB structures showed more strain rate sensitivity at high temperatures than at low temperatures. 

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5. Development and validation of ReaxFF forcefield for solid-state ion conduction in Ag/S-based systems.

   Anderson, C. J. ( April 2021 , National Meeting of the American Chemical Society)

   null (Ed.)

   Abstract: Solid-state ion conduction (SSIC) is a mechanism of ionic current that has garnered increasing attention for applications in all-solid-state batteries and atomic switches. The Ag/S SSIC system in β-Ag S, possessing the highest ionic conductivity of any known material, provides a unique opportunity to better understand the fundamental nature of SSIC. β-Ag S is topographically similar to binary perovskites except that it is cubic, leading to isotropic SSIC exceeding 4 S/cm. The dynamic nature of SSIC makes it difficult to study by observational means, where inherent time-averaging obscures correlations among atomic transit routes.Molecular dynamics (MD) is a tool ideally suited for gaining insight into large atomic systems with subnanosecond time resolutions. However, traditional MD potentials lack a description of bond-breaking/forming reactions, which are an essential aspect of SSIC and related memristic properties. This limitation can be overcome by using a reactive force field (ReaxFF), which enables the simulation of bonding reactions with DFT-level accuracy. In this study, we present a ReaxFF force field for the Ag/S system, optimized for simulating SSIC in β-Ag S. Training data consisted of crystal structures, Bader partial charges, and energies of various Ag/S clusters calculated at the DFT-level. Energies were obtained with Gaussian 16, using the PBEh1PBE hybrid functional with a triple-zeta correlation-consistent basis set. Multiobjective parameter optimization was accomplished with an updated form of the Genetic Algorithm for Reactive Force Fields (GARFfield). The force field was validated with potential energy and ion conductivity calculations, along with relevant structural features. Results were compared with equivalent simulations from other established potentials. This new ReaxFF force field will enable modeling of realistic SSIC configurations for Ag/S-based materials and provides a viable approach for extending ReaxFF to other SSIC systems in the future. This work was supported by the National Science Foundation under grant #2025319. 

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