CHARMM-GUI Nanomaterial Modeler for Modeling and Simulation of Nanomaterial Systems

Weakly ionized gold nanoparticles amplify immunoassays for ultrasensitive point-of-care sensors

Gold nanoparticle-based lateral flow immunoassays (AuNP LFIAs) are widely used point-of-care (POC) sensors for in vitro diagnostics. However, the sensitivity limitation of conventional AuNP LFIAs impedes the detection of trace biomarkers. Several studies have explored the size and shape factors of AuNPs and derivative nanohybrids, showing limited improvements or enhanced sensitivity at the cost of convenience and affordability. Here, we investigated surface chemistry on the sensitivity of AuNP LFIAs. By modifying surface ligands, a surface chemistry strategy involving weakly ionized AuNPs enables ultrasensitive naked-eye LFIAs (~100-fold enhanced sensitivity). We demonstrated how this surface chemistry-amplified immunoassay approach modulates nanointerfacial bindings to promote antibody adsorption and higher activity of adsorbed antibodies. This surface chemistry design eliminates complex nanosynthesis, auxiliary devices, or additional reagents while efficiently improving sensitivity with advantages: simplified fabrication process, excellent reproducibility and reliability, and ultrasensitivity toward various biomarkers. The surface chemistry using weakly ionized AuNPs represents a versatile approach for sensitizing POC sensors.

CHARMM-GUI Multicomponent Assembler for modeling and simulation of complex multicomponent systems

Atomic-scale molecular modeling and simulation are powerful tools for computational biology. However, constructing models with large, densely packed molecules, non-water solvents, or with combinations of multiple biomembranes, polymers, and nanomaterials remains challenging and requires significant time and expertise. Furthermore, existing tools do not support such assemblies under the periodic boundary conditions (PBC) necessary for molecular simulation. Here, we describe Multicomponent Assembler in CHARMM-GUI that automates complex molecular assembly and simulation input preparation under the PBC. In this work, we demonstrate its versatility by preparing 6 challenging systems with varying density of large components: (1) solvated proteins, (2) solvated proteins with a pre-equilibrated membrane, (3) solvated proteins with a sheet-like nanomaterial, (4) solvated proteins with a sheet-like polymer, (5) a mixed membrane-nanomaterial system, and (6) a sheet-like polymer with gaseous solvent. Multicomponent Assembler is expected to be a unique cyberinfrastructure to study complex interactions between small molecules, biomacromolecules, polymers, and nanomaterials.

Cell-inspired, massive electromodulation of friction via transmembrane fields across lipid bilayers

Transient electric fields across cell bilayer membranes can lead to electroporation and cell fusion, effects crucial to cell viability whose biological implications have been extensively studied. However, little is known about these behaviours in a materials context. Here we find that transmembrane electric fields can lead to a massive, reversible modulation of the sliding friction between surfaces coated with lipid-bilayer membranes-a 200-fold variation, up to two orders of magnitude greater than that achieved to date. Atomistic simulations reveal that the transverse fields, resembling those at cell membranes, lead to fully reversible electroporation of the confined bilayers and the formation of inter-bilayer bridges analogous to the stalks preceding intermembrane fusion. These increase the interfacial dissipation through reduced hydration at the slip plane, forcing it to revert in part from the low-dissipation, hydrated lipid-headgroup plane to the intra-bilayer, high-dissipation acyl tail interface. Our results demonstrate that lipid bilayers under transmembrane electric fields can have striking materials modification properties.

Chitin Nanofibers Enable the Colloidal Dispersion of Carbon Nanomaterials in Aqueous Phase and Hybrid Material Coassembly

Chitin nanofibrils (ChNF) sourced from discarded marine biomass are shown as effective stabilizers of carbon nanomaterials in aqueous media. Such stabilization is evaluated for carbon nanotubes (CNT) considering spatial and temporal perspectives by using experimental (small-angle X-ray scattering, among others) and theoretical (atomistic simulation) approaches. We reveal that the coassembly of ChNF and CNT is governed by hydrophobic interactions, while electrostatic repulsion drives the colloidal stabilization of the hybrid ChNF/CNT system. Related effects are found to be transferable to multiwalled carbon nanotubes and graphene nanosheets. The observations explain the functionality of hybrid membranes obtained by aqueous phase processing, which benefit from an excellent areal mass distribution (correlated to piezoresistivity), also contributing to high electromechanical performance. The water resistance and flexibility of the ChNF/CNT membranes (along with its tensile strength at break of 190 MPa, conductivity of up to 426 S/cm, and piezoresistivity and light absorption properties) are conveniently combined in a device demonstration, a sunlight water evaporator. The latter is shown to present a high evaporation rate (as high as 1.425 kg water m-2 h-1 under one sun illumination) and recyclability.

Mechanistic Insights Behind the Self-Assembly of Human Insulin under the Influence of Surface-Engineered Gold Nanoparticles

Elucidating the underlying principles of amyloid protein self-assembly at nanobio interfaces is extremely challenging due to the diversity in physicochemical properties of nanomaterials and their physical interactions with biological systems. It is, therefore, important to develop nanoscale materials with dynamic features and heterogeneities. In this work, through engineering of hierarchical polyethylene glycol (PEG) structures on gold nanoparticle (GNP) surfaces, tailored nanomaterials with different surface properties and conformations (GNPs-PEG) are created for modulating the self-assembly of a widely studied protein, insulin, under amyloidogenic conditions. Important biophysical studies including thioflavin T (ThT) binding, circular dichroism (CD), surface plasmon resonance (SPR), and atomic force microscopy (AFM) showed that higher-molecular weight GNPs-PEG triggered the formation of amyloid fibrils by promoting adsorption of proteins at nanoparticle surfaces and favoring primary nucleation rate. Moreover, the modulation of fibrillation kinetics reduces the overall toxicity of insulin oligomers and fibrils. In addition, the interaction between the PEG polymer and amyloidogenic insulin examined using MD simulations revealed major changes in the secondary structural elements of the B chain of insulin. The experimental findings provide molecular-level descriptions of how the PEGylated nanoparticle surface modulates protein adsorption and drives the self-assembly of insulin. This facile approach provides a new avenue for systematically altering the binding affinities on nanoscale surfaces by tailoring their topologies for examining adsorption-induced fibrillogenesis phenomena of amyloid proteins. Together, this study suggests the role of nanobio interfaces during surface-induced heterogeneous nucleation as a primary target for designing therapeutic interventions for amyloid-related neurodegenerative disorders.

Estimating Binding Energies of π-Stacked Aromatic Dimers Using Force Field-Driven Molecular Dynamics

π-π stacking are omnipresent interactions, crucial in many areas of chemistry, and often studied using quantum chemical methods. Here, we report a simple and computationally efficient method of estimating the binding energies of stacked polycyclic aromatic hydrocarbons based on steered molecular dynamics. This method leverages the force field parameters for accurate calculation. The presented results show good agreement with those obtained through DFT at the ωB97X-D3/cc-pVQZ level of theory. It is demonstrated that this force field-driven SMD method can be applied to other aromatic molecules, allowing insight into the complexity of the stacking interactions and, more importantly, reporting π-π stacking energy values with reasonable precision.

Fabrication of High-Negatively Charged Bicelle-Mediated Supported Lipid Bilayer

Supported lipid bilayers (SLBs), two-dimensional lipid films formed on a solid-supporting substrate, serve as models for biomembranes and exhibit remarkable potential in chemistry, biology, and medicine. However, preparing SLBs with highly negatively charged contents on the negatively charged surface by overcoming electrostatic repulsion remains a challenge. Here, a creative bicelle-mediated and divalent cation-free SLB preparation method with the assistance of phosphate-buffered saline (PBS) solution was proposed, which can form the SLBs containing 50% DOPS or 30% CL on the silica surface monitored by a quartz crystal microbalance with dissipation (QCM-D). Results of molecular dynamics (MD) simulation indicate that electrostatic repulsion can be overcome by the increased number of hydrogen bonds caused by the adsorption of dihydrogen phosphate ions onto the headgroups of lipids. In addition, the negatively charged SLB formation was identified to be a three-step kinetic process, which differs from a two-step mechanism in the case of amphoteric SLB. The extra kinetic step can be attributed to the reduction in the number of intermolecular hydrogen bonds and the ordering of water molecules in the hydration layer. This investigation resolves the challenge of fabricating SLB over negatively charged surfaces and offers a fresh perspective on the SLB assembly methodology.

Nanoparticle Metrology of Silicates Using Time-Resolved Multiplexed Dye Fluorescence Anisotropy, Small Angle X-ray Scattering, and Molecular Dynamics Simulations

We investigate the nanometrology of sub-nanometre particle sizes in industrially manufactured sodium silicate liquors at high pH using time-resolved fluorescence anisotropy. Rather than the previous approach of using a single dye label, we investigate and quantify the advantages and limitations of multiplexing two fluorescent dye labels. Rotational times of the non-binding rhodamine B and adsorbing rhodamine 6G dyes are used to independently determine the medium microviscosity and the silicate particle radius, respectively. The anisotropy measurements were performed on the range of samples prepared by diluting the stock solution of silicate to concentrations ranging between 0.2 M and 2 M of NaOH and on the stock solution at different temperatures. Additionally, it was shown that the particle size can also be measured using a single excitation wavelength when both dyes are present in the sample. The recovered average particle size has an upper limit of 7.0 ± 1.2 Å. The obtained results were further verified using small-angle X-ray scattering, with the recovered particle size equal to 6.50 ± 0.08 Å. To disclose the impact of the dye label on the measured complex size, we further investigated the adsorption state of rhodamine 6G on silica nanoparticles using molecular dynamics simulations, which showed that the size contribution is strongly impacted by the size of the nanoparticle of interest. In the case of the higher radius of curvature (less curved) of larger particles, the size contribution of the dye label is below 10%, while in the case of smaller and more curved particles, the contribution increases significantly, which also suggests that the particles of interest might not be perfectly spherical.

Type Label Framework for Bonded Force Fields in LAMMPS

New functionality is added to the LAMMPS molecular simulation package, which increases the versatility with which LAMMPS can interface with supporting software and manipulate information associated with bonded force fields. We introduce the "type label" framework that allows atom types and their higher-order interactions (bonds, angles, dihedrals, and impropers) to be represented in terms of the standard atom type strings of a bonded force field. Type labels increase the human readability of input files, enable bonded force fields to be supported by the OpenKIM repository, simplify the creation of reaction templates for the REACTER protocol, and increase compatibility with external visualization tools, such as VMD and OVITO. An introductory primer on the forms and use of bonded force fields is provided to motivate this new functionality and serve as an entry point for LAMMPS and OpenKIM users unfamiliar with bonded force fields. The type label framework has the potential to streamline modeling workflows that use LAMMPS by increasing the portability of software, files, and scripts for preprocessing, running, and postprocessing a molecular simulation.

Green-engineered clay- and carbon-based composite materials for the adsorption of benzene from air

Benzene is a carcinogenic volatile organic compound (VOC) that is ubiquitously detected in enclosed spaces due to emissions from cooking activities, building materials, and cleaning products. To remove benzene and other VOCs from indoor air and protect public health, traditional fabric filters have been modified to contain activated carbons to enhance the filtration efficacy. In this study, composites derived from natural clay minerals and activated carbon were individually green-engineered with chlorophylls and were attached to the surface of filter materials. These systems were assessed for their adsorption of benzene from air using in vitro and in silico methods. Isothermal, thermodynamic, and kinetic experiments indicated that all green-engineered composites had improved binding profiles for benzene, as demonstrated by increased binding affinities (Kf ≥ 900 vs 472) and lower values of Gibbs free energy (ΔG = -16.8 vs -15.2) compared to activated carbon. Adsorption of benzene to all composites was achieved quickly (< 30 min), and the green-engineered composites also showed low levels of desorption (≤ 25%). While free chlorophyll is known to be photosensitive, chlorophylls in the green-engineered composites showed photostability and maintained high binding rates (≥ 70%). Additionally, the in silico simulations demonstrated the significant contribution of chlorophyll for the overall binding of benzene in clay systems and that chlorophyll could contribute to benzene binding in the carbon-based systems. Together, these studies indicated that novel, green-engineered composite materials can be effective filter sorbents to enhance the removal of benzene from air.

Adsorption and removal of polystyrene nanoplastics from water by green-engineered clays

Human exposure to micro- and nanoplastics (MNPs) commonly occurs through the consumption of contaminated drinking water. Among these, polystyrene (PS) is well-characterized and is one of the most abundant MNPs, accounting for 10 % of total plastics. Previous studies have focused on carbonaceous materials to remove MNPs by filtration, but most of the work has involved microplastics since nanoplastics (NPs) are smaller in size and more difficult to measure and remove. To address this need, green-engineered chlorophyll-amended sodium and calcium montmorillonites (SMCH and CMCH) were tested for their ability to bind and detoxify parent and fluorescently labeled PSNP using in vitro, in silico, and in vivo assays. In vitro dosimetry, isothermal analyses, thermodynamics, and adsorption/desorption kinetic models demonstrated 1) high binding capacities (173-190 g/kg), 2) high affinities (103), and 3) chemisorption as suggested by low desorption (≤42 %) and high Gibbs free energy and enthalpy (>|-20| kJ/mol) in the Langmuir and pseudo-second-order models. Computational dynamics simulations for 30 and 40 monomeric units of PSNP depicted that chlorophyll amendments increased the binding percentage and contributed to the sustained binding. Also, 64 % of PSNP bind to both the head and tail of chlorophyll aggregates, rather than the head or tail only. Fluorescent PSNP at 100 nm and 30 nm that were exposed to Hydra vulgaris showed concentration-dependent toxicity at 20-100 µg/mL. Importantly, the inclusion of 0.05-0.3 % CMCH and SMCH significantly (p ≤ 0.01) and dose-dependently reduced PSNP toxicity in morphological changes and feeding rate. The bioassay validated the in vitro and in silico predictions about adsorption efficacy and mechanisms and suggested that CMCH and SMCH are efficacious binders for PSNP in water.

The Effect of Acidic Residues on the Binding between Opicalcin1 and Ryanodine Receptor from the Structure-Functional Analysis

Calcin is a group ligand with high affinity and specificity for the ryanodine receptors (RyRs). Little is known about the effect of its acidic residues on the spacial structure as well as the interaction with RyRs. We screened the opicalcin1 acidic mutants and investigated the effect of mutation on activity. The results indicated that all acidic mutants maintained the structural features, but their surface charge distribution underwent significant changes. Molecular docking and dynamics simulations were used to analyze the interaction between opicalcin1 mutants and RyRs, which demonstrated that all opicalcin1 mutants effectively bound to the channel domain of RyR1. This stable binding induced a pronounced asymmetry in the structure of the RyR tetramer, exhibiting a high degree of structural dissimilarity. [3H]Ryanodine binding to RyR1 was enhanced in D2A and D15A, which was similar to opicalcin1, but that effect was suppressed in E12A and E29A and reversed for the DE-4A, thereby inhibiting ryanodine binding. Opicalcin1 and DE-4A also exhibited the ability to form stable docking structures with RyR2. Acidic residues play a crucial role in the structure of calcin and its functional interaction with RyRs that is beneficial for the calcin optimization to develop more active peptide lead compounds for RyR-related diseases.

Osteocalcin: Promoter or Inhibitor of Hydroxyapatite Growth?

Osteocalcin is the most abundant noncollagenous bone protein and the functions in bone remineralization as well as in inhibition of bone growth have remained unclear. In this contribution, we explain the dual role of osteocalcin in the nucleation of new calcium phosphate during bone remodeling and in the inhibition of hydroxyapatite crystal growth at the molecular scale. The mechanism was derived using pH-resolved all-atom models for the protein, phosphate species, and hydroxyapatite, along with molecular dynamics simulations and experimental and clinical observations. Osteocalcin binds to (hkl) hydroxyapatite surfaces through multiple residues, identified in this work, and the fingerprint of binding residues varies as a function of the (hkl) crystal facet and pH value. On balance, the affinity of osteocalcin to hydroxyapatite slows down crystal growth. The unique tricalcium γ-carboxylglutamic acid (Gla) domain hereby rarely adsorbs to hydroxyapatite surfaces and faces instead toward the solution. The Gla domain enables prenucleation of calcium phosphate for new bone formation at a slightly acidic pH of 5. The growth of prenucleation clusters of calcium phosphate continues upon increase in pH value from 5 to 7 and is much less favorable, or not observed, on the native osteocalcin structure at and above neutral pH values of 7. The results provide mechanistic insight into the early stages of bone remodeling from the molecular scale, help inform mutations of osteocalcin to modify binding to apatites, support drug design, and guide toward potential cures for osteoporosis and hyperosteogeny.

Impact of the Crystal Structure of Silica Nanoparticles on Rhodamine 6G Adsorption: A Molecular Dynamics Study

Understanding the mechanism of adsorption of Rhodamine 6G (R6G) to various crystal structures of silica nanoparticles (SNPs) is important to elucidate the impact of dye size when measuring the size of the dye-SNP complex via the time-resolved fluorescence anisotropy method. In this work, molecular dynamics (MD) simulations were used to get an insight into the R6G adsorption process, which cannot be observed using experimental methods. It was found that at low pH, α-Cristobalite structured SNPs have a strong affinity to R6G; however, at high pH, more surface silanol groups undergo ionization when compared with α-Quartz, preventing the adsorption. Therefore, α-Quartz structured SNPs are more suitable for R6G adsorption at high pH than the α-Cristobalite ones. Furthermore, it was found that stable adsorption can occur only when the R6G xanthene core is oriented flat with respect to the SNP surface, indicating that the dye size does not contribute significantly to the measured size of the dye-SNP complex. The requirement of correct dipole moment orientation indicates that only one R6G molecule can adsorb on any sized SNP, and the R6G layer formation on SNP is not possible. Moreover, the dimerization process of R6G and its competition with the adsorption has been explored. It has been shown that the highest stable R6G aggregate is a dimer, and in this form, R6G does not adsorb to SNPs. Finally, using steered molecular dynamics (SMD) with constant-velocity pulling, the binding energies of R6G dimers and R6G complexes with both α-Quartz and α-Cristobalite SNPs of 40 Å diameter were estimated. These confirm that R6G adsorption is most stable on 40 Å α-Quartz at pH 7, although dimerization is equally possible.

Accurate Force Fields for Atomistic Simulations of Oxides, Hydroxides, and Organic Hybrid Materials up to the Micrometer Scale

The simulation of metals, oxides, and hydroxides can accelerate the design of therapeutics, alloys, catalysts, cement-based materials, ceramics, bioinspired composites, and glasses. Here we introduce the INTERFACE force field (IFF) and surface models for α-Al2O3, α-Cr2O3, α-Fe2O3, NiO, CaO, MgO, β-Ca(OH)2, β-Mg(OH)2, and β-Ni(OH)2. The force field parameters are nonbonded, including atomic charges for Coulomb interactions, Lennard-Jones (LJ) potentials for van der Waals interactions with 12-6 and 9-6 options, and harmonic bond stretching for hydroxide ions. The models outperform DFT calculations and earlier atomistic models (Pedone, ReaxFF, UFF, CLAYFF) up to 2 orders of magnitude in reliability, compatibility, and interpretability due to a quantitative representation of chemical bonding consistent with other compounds across the periodic table and curated experimental data for validation. The IFF models exhibit average deviations of 0.2% in lattice parameters, <10% in surface energies (to the extent known), and 6% in bulk moduli relative to experiments. The parameters and models can be used with existing parameters for solvents, inorganic compounds, organic compounds, biomolecules, and polymers in IFF, CHARMM, CVFF, AMBER, OPLS-AA, PCFF, and COMPASS, to simulate bulk oxides, hydroxides, electrolyte interfaces, and multiphase, biological, and organic hybrid materials at length scales from atoms to micrometers. The nonbonded character of the models also enables the analysis of mixed oxides, glasses, and certain chemical reactions, and well-performing nonbonded models for silica phases, SiO2, are introduced. Automated model building is available in the CHARMM-GUI Nanomaterial Modeler. We illustrate applications of the models to predict the structure of mixed oxides, and energy barriers of ion migration, as well as binding energies of water and organic molecules in outstanding agreement with experimental data and calculations at the CCSD(T) level. Examples of model building for hydrated, pH-sensitive oxide surfaces to simulate solid-electrolyte interfaces are discussed.

Osmolytes as Cryoprotectants under Salt Stress

Cryoprotecting agent (CPA)-guided preservation is essential for effective protection of cells from cryoinjuries. However, current cryoprotecting technologies practiced to cryopreserve cells for biomedical applications are met with extreme challenges due to the associated toxicity of CPAs. Because of these limitations of present CPAs, the quest for nontoxic alternatives for useful application in cell-based biomedicines has been attracting growing interest. Toward this end, here, we investigate naturally occurring osmolytes' scope as biocompatible cryoprotectants under cold stress conditions in high-saline medium. Via a combination of the simulation and experiment on charged silica nanostructures, we render first-hand evidence that a pair of archetypal osmolytes, glycine and betaine, would act as a cryoprotectant by restoring the indigenous intersurface electrostatic interaction, which had been a priori screened due to the cold effect under salt stress. While these osmolytes' individual modes of action are sensitive to subtle chemical variation, a uniform augmentation in the extent of osmolytic activity is observed with an increase in temperature to counter the proportionately enhanced salt screening. The trend as noted in inorganic nanostructures is found to be recurrent and robustly transferable in a charged protein interface. In hindsight, our observation justifies the sufficiency of the reduced requirement of osmolytes in cells during critical cold conditions and encourages their direct usage and biomimicry for cryopreservation.

Simulation of gold nanoparticle movement through normal and cancer cell membranes

Gold nanoparticles (Au-NPs) have been used for a long time to target cancer cells. Different modalities have been suggested to utilize Au-NPs in cancer patients. We construct both normal and cancer cell membranes to simulate the Au-NP entry to understand better how it can penetrate the cancer cell membrane. We use molecular dynamics simulation (MDS) on both normal and cancer cell membrane models for 150 ns. At the same time, we prepared the Au-NP of spherical shape (16 nm radius) capped with citrate using MDS for 100 ns. Finally, we added the Au-NP close to the membranes and moved it using 1000 kJ mol-1 nm-1 force constant during the 7.7 ns MDS run. We analyzed the membranes in the presence and absence of the Au-NP and compared normal and cancer membranes. The results show that normal cell membranes have higher stability than cancer membranes. Additionally, Au-NP forms pore in the membranes that facilitate water and ions entry during the movement inside the lipid bilayer region. These pores are responsible for the enhanced response of Au-NP-loaded chemotherapeutic agents in cancer treatment.

CHARMM-GUI Multicomponent Assembler for Modeling and Simulation of Complex Multicomponent Systems

Atomic-scale molecular modeling and simulation are powerful tools for computational biology. However, constructing models with large, densely packed molecules, non-water solvents, or with combinations of multiple biomembranes, polymers, and nanomaterials remains challenging and requires significant time and expertise. Furthermore, existing tools do not support such assemblies under the periodic boundary conditions (PBC) necessary for molecular simulation. Here, we describe Multicomponent Assembler in CHARMM-GUI that automates complex molecular assembly and simulation input preparation under the PBC. We demonstrate its versatility by preparing 6 challenging systems with varying density of large components: (1) solvated proteins, (2) solvated proteins with a pre-equilibrated membrane, (3) solvated proteins with a sheet-like nanomaterial, (4) solvated proteins with a sheet-like polymer, (5) a mixed membrane-nanomaterial system, and (6) a sheet-like polymer with gaseous solvent. Multicomponent Assembler is expected to be a unique cyberinfrastructure to facilitate innovative studies of complex interactions between small (organic and inorganic) molecules, biomacromolecules, polymers, and nanomaterials.

Machine-learning based prediction of small molecule-surface interaction potentials

Predicting the adsorption affinity of a small molecule to a target surface is of importance to a range of fields, from catalysis to drug delivery and human safety, but a complex task to perform computationally when taking into account the effects of the surrounding medium. We present a flexible machine-learning approach to predict potentials of mean force (PMFs) and adsorption energies for chemical-surface pairs from the separate interaction potentials of each partner with a set of probe atoms. We use a pre-existing library of PMFs obtained via atomistic molecular dynamics simulations for a variety of inorganic materials and molecules to train the model. We find good agreement between original and predicted PMFs in both training and validation groups, confirming the predictive power of this approach, and demonstrate the flexibility of the model by producing PMFs for molecules and surfaces outside the training set.

CHARMM-GUI PDB Manipulator: Various PDB Structural Modifications for Biomolecular Modeling and Simulation

Molecular modeling and simulation play important roles in biomedical research as they provide molecular-level insight into the underlying mechanisms of biological functions that are difficult to elucidate only with experiments. CHARMM-GUI (https://charmm-gui.org) is a web-based cyberinfrastructure that is widely used to generate various molecular simulation system and input files and thus facilitates and standardizes the usage of common and advanced simulation techniques. In particular, PDB Manipulator provides various chemical modification options as the starting point for most input generation modules in CHARMM-GUI. Here, we discuss recent additions to PDB Manipulator, such as non-standard amino acids/RNA substitutions, ubiquitylation and SUMOylation, Lys/Arg post-translational modifications, lipidation, peptide stapling, and improved parameterization options of small molecules. These additional features are expected to make complex PDB modifications easy for biomolecular modeling and simulation.

Entropic barrier of water permeation through single-file channels

Facilitated water permeation through narrow biological channels is fundamental for all forms of life. Despite its significance in health and disease as well as for biotechnological applications, the energetics of water permeation are still elusive. Gibbs free energy of activation is composed of an enthalpic and an entropic component. Whereas the enthalpic contribution is readily accessible via temperature dependent water permeability measurements, estimation of the entropic contribution requires information on the temperature dependence of the rate of water permeation. Here, we estimate, by means of accurate activation energy measurements of water permeation through Aquaporin-1 and by determining the accurate single channel permeability, the entropic barrier of water permeation through a narrow biological channel. Thereby the calculated value for [Formula: see text] = 2.01 ± 0.82 J/(mol·K) links the activation energy of 3.75 ± 0.16 kcal/mol with its efficient water conduction rate of ~10¹⁰ water molecules/second. This is a first step in understanding the energetic contributions in various biological and artificial channels exhibiting vastly different pore geometries.

pyCHARMM: Embedding CHARMM Functionality in a Python Framework

CHARMM is rich in methodology and functionality as one of the first programs addressing problems of molecular dynamics and modeling of biological macromolecules and their partners, e.g., small molecule ligands. When combined with the highly developed CHARMM parameters for proteins, nucleic acids, small molecules, lipids, sugars, and other biologically relevant building blocks, and the versatile CHARMM scripting language, CHARMM has been a trendsetting platform for modeling studies of biological macromolecules. To further enhance the utility of accessing and using CHARMM functionality in increasingly complex workflows associated with modeling biological systems, we introduce pyCHARMM, Python bindings, functions, and modules to complement and extend the extensive set of modeling tools and methods already available in CHARMM. These include access to CHARMM function-generated variables associated with the system (psf), coordinates, velocities and forces, atom selection variables, and force field related parameters. The ability to augment CHARMM forces and energies with energy terms or methods derived from machine learning or other sources, written in Python, CUDA, or OpenCL and expressed as Python callable routines is introduced together with analogous functions callable during dynamics calculations. Integration of Python-based graphical engines for visualization of simulation models and results is also accessible. Loosely coupled parallelism is available for workflows such as free energy calculations, using MBAR/TI approaches or high-throughput multisite λ-dynamics (MSλD) free energy methods, string path optimization calculations, replica exchange, and molecular docking with a new Python-based CDOCKER module. CHARMM accelerated platform kernels through the CHARMM/OpenMM API, CHARMM/DOMDEC, and CHARMM/BLaDE API are also readily integrated into this Python framework. We anticipate that pyCHARMM will be a robust platform for the development of comprehensive and complex workflows utilizing Python and its extensive functionality as well as an optimal platform for users to learn molecular modeling methods and practices within a Python-friendly environment such as Jupyter Notebooks.

Emerging Trends of Computational Chemistry and Molecular Modeling in Froth Flotation: A Review

Froth flotation is the most versatile process in mineral beneficiation, extensively used to concentrate a wide range of minerals. This process comprises mixtures of more or less liberated minerals, water, air, and various chemical reagents, involving a series of intermingled multiphase physical and chemical phenomena in the aqueous environment. Today's main challenge facing the froth flotation process is to gain atomic-level insights into the properties of its inherent phenomena governing the process performance. While it is often challenging to determine these phenomena via trial-and-error experimentations, molecular modeling approaches not only elicit a deeper understanding of froth flotation but can also assist experimental studies in saving time and budget. Thanks to the rapid development of computer science and advances in high-performance computing (HPC) infrastructures, theoretical/computational chemistry has now matured enough to successfully and gainfully apply to tackle the challenges of complex systems. In mineral processing, however, advanced applications of computational chemistry are increasingly gaining ground and demonstrating merit in addressing these challenges. Accordingly, this contribution aims to encourage mineral scientists, especially those interested in rational reagent design, to become familiarized with the necessary concepts of molecular modeling and to apply similar strategies when studying and tailoring properties at the molecular level. This review also strives to deliver the state-of-the-art integration and application of molecular modeling in froth flotation studies to assist either active researchers in this field to disclose new directions for future research or newcomers to the field to initiate innovative works.

Wrapping-Trapping versus Extraction Mechanism of Bactericidal Activity of MoS2 Nanosheets against Staphylococcus aureus Bacterial Membrane

The promising broad-spectrum antibacterial activity of two-dimensional molybdenum disulfide (2D MoS₂) has been widely recognized in the past decade. However, a comprehensive understanding of how the antibacterial pathways opted by the MoS₂ nanosheets varies with change in lipid compositions of different bacterial strains is imperative to harness their full antibacterial potential and remains unexplored thus far. Herein, we present an atomistic molecular dynamics (MD) study to investigate the distinct modes of antibacterial action of MoS₂ nanosheets against Staphylococcus aureus (S. aureus) under varying conditions. We observed that the freely dispersed nanosheets readily adhered to the bacterial membrane outer surface and opted for an unconventional surface directed "wrapping-trapping" mechanism at physiological temperature (i.e., 310 K). The adsorbed nanosheets mildly influenced the membrane structure by originating a compact packing of the lipid molecules present in its direct contact. Interestingly, these surface adsorbed nanosheets exhibited extensive phospholipid extraction to their surface, thereby inducing transmembrane water passage analogous to the cellular leakage, even at a slight increment of 20 K in the temperature. The strong van der Waals interactions between lipid fatty acyl tails and MoS₂ basal planes were primarily responsible for this destructive phospholipid extraction. In addition, the MoS₂ nanosheets bound to an imaginary substrate, controlling their vertical alignment, demonstrated a "nano-knives" action by spontaneously piercing inside the membrane core through their sharp corner, subsequently causing localized lipid ordering in their vicinity. The larger nanosheet produced a more profound deteriorating impact in all of the observed mechanisms. Keeping the existing knowledge about the bactericidal activity of 2D MoS₂ in view, our study concludes that their antibacterial activity is strongly governed by the lipid composition of the bacterial membrane and can be intensified either by controlling the nanosheet vertical alignment or by moderately warming up the systems.

Insight into the Binding Mechanisms of Quartz-Selective Peptides: Toward Greener Flotation Processes

Mining practices, chiefly froth flotation, are being critically reassessed to replace their use of biohazardous chemical reagents in favor of biofriendly alternatives as a path toward green processes. In this regard, this study aimed at evaluating the interactions of peptides, as potential floatation collectors, with quartz using phage display and molecular dynamics (MD) simulations. Quartz-selective peptide sequences were initially identified by phage display at pH = 9 and further modeled by a robust simulation scheme combining classical MD, replica exchange MD, and steered MD calculations. Our residue-specific analyses of the peptides revealed that positively charged arginine and lysine residues were favorably attracted by the quartz surface at basic pH. The negatively charged residues at pH 9 (i.e., aspartic acid and glutamic acid) further showed affinity toward the quartz surface through electrostatic interactions with the positively charged surface-bound Na⁺ ions. The best-binding heptapeptide combinations, however, contained both positively and negatively charged residues in their composition. The flexibility of peptide chains was also shown to directly affect the adsorption behavior of the peptide. While attractive intrapeptide interactions were dominated by a weak peptide-quartz binding, the repulsive self-interactions in the peptides improved the binding propensity to the quartz surface. Our results showed that MD simulations are fully capable of revealing mechanistic details of peptide adsorption to inorganic surfaces and are an invaluable tool to accelerate the rational design of peptide sequences for mineral processing applications.

CHARMM-GUI Membrane Builder: Past, Current, and Future Developments and Applications

Molecular dynamics simulations of membranes and membrane proteins serve as computational microscopes, revealing coordinated events at the membrane interface. As G protein-coupled receptors, ion channels, transporters, and membrane-bound enzymes are important drug targets, understanding their drug binding and action mechanisms in a realistic membrane becomes critical. Advances in materials science and physical chemistry further demand an atomistic understanding of lipid domains and interactions between materials and membranes. Despite a wide range of membrane simulation studies, generating a complex membrane assembly remains challenging. Here, we review the capability of CHARMM-GUI Membrane Builder in the context of emerging research demands, as well as the application examples from the CHARMM-GUI user community, including membrane biophysics, membrane protein drug-binding and dynamics, protein-lipid interactions, and nano-bio interface. We also provide our perspective on future Membrane Builder development.

A Micro-In-Macro Gastroretentive System for the Delivery of Narrow-Absorption Window Drugs

A micro-in-macro gastroretentive and gastrofloatable drug delivery system (MGDDS), loaded with the model-drug ciprofloxacin, was developed in this study to address the limitations commonly experienced in narrow-absorption window (NAW) drug delivery. The MGDDS, which consists of microparticles loaded in a gastrofloatable macroparticle (gastrosphere) was designed to modify the release of ciprofloxacin, allowing for an increased drug absorption via the gastrointestinal tract. The prepared inner microparticles (1–4 µm) were formed by crosslinking chitosan (CHT) and Eudragit® RL 30D (EUD), with the outer gastrospheres prepared from alginate (ALG), pectin (PEC), poly(acrylic acid) (PAA) and poly(lactic-co-glycolic) acid (PLGA). An experimental design was utilized to optimize the prepared microparticles prior to Fourier Transition Infrared (FTIR) spectroscopy, Scanning Electron Microscopy (SEM) and in vitro drug release studies. Additionally, the in vivo analysis of the MGDDS, employing a Large White Pig model and molecular modeling of the ciprofloxacin-polymer interactions, were performed. The FTIR results determined that the crosslinking of the respective polymers in the microparticle and gastrosphere was achieved, with the SEM analysis detailing the size of the microparticles formed and the porous nature of the MGDDS, which is essential for drug release. The in vivo drug release analysis results further displayed a more controlled ciprofloxacin release profile over 24 h and a greater bioavailability for the MGDDS when compared to the marketed immediate-release ciprofloxacin product. Overall, the developed system successfully delivered ciprofloxacin in a control-release manner and enhanced its absorption, thereby displaying the potential of the system to be used in the delivery of other NAW drugs.

Pharmacokinetic Study of Triptolide Nanocarrier in Transdermal Drug Delivery System-Combination of Experiment and Mathematical Modeling

Compared with traditional oral and injection administration, the transdermal administration of traditional Chinese medicine has distinctive characteristics and advantages, which can avoid the "first pass effect" of the liver and the destruction of the gastrointestinal tract, maintain a stable blood concentration, and prolong drug action time. However, the basic theory and technology research in transdermal drug delivery are relatively limited at present, especially regarding research on new carriers of transdermal drug delivery and pharmacokinetic studies of the skin, which has become a bottleneck of transdermal drug delivery development. Triptolide is one of the main active components of Tripterygium wilfordii, which displays activities against mouse models of polycystic kidney disease and pancreatic cancer but its physical properties and severe toxicity limit its therapeutic potential. Due to the previously mentioned advantages of transdermal administration, in this study, we performed a detail analysis of the pharmacokinetics of a new transdermal triptolide delivery system. Triptolide nanoemulsion gels were prepared and served as new delivery systems, and the ex vivo characteristics were described. The metabolic characteristics of the different triptolide transdermal drug delivery formulations were investigated via skin-blood synchronous microdialysis combined with LC/MS. A multiscale modeling framework, molecular dynamics and finite element modeling were adopted to simulate the transport process of triptolide in the skin and to explore the pharmacokinetics and mathematical patterns. This study shows that the three-layer model can be used for transdermal drug delivery system drug diffusion research. Therefore, it is profitable for transdermal drug delivery system design and the optimization of the dosage form. Based on the drug concentration of the in vivo microdialysis measurement technology, the diffusion coefficient of drugs in the skin can be more accurately measured, and the numerical results can be verified. Therefore, the microdialysis technique combined with mathematical modeling provides a very good platform for the further study of transdermal delivery systems. This research will provide a new technology and method for the study of the pharmacokinetics of traditional Chinese medicine transdermal drug delivery. It has important theoretical and practical significance in clarifying the metabolic transformation of percutaneous drug absorption and screening for appropriate drugs and dosage forms of transdermal drug delivery.

Polystyrene-modified carbon nanotubes: Promising carriers in targeted drug delivery

To design drug-delivery agents for therapeutic and diagnostic applications, understanding the mechanisms by which covalently functionalized carbon nanotubes penetrate and interact with cell membranes is of great importance. Here, we report all-atom molecular dynamics results from polystyrene and carboxyl-terminated polystyrene-modified carbon nanotubes and show their translocation behavior across a model lipid bilayer together with their potential to deliver a molecule of the drug ibuprofen into the cell. Our results indicate that functionalized carbon nanotubes are internalized by the membrane in hundreds of nanoseconds and that drug loading increases the internalization speed further. Both loaded and unloaded tubes cross the closest leaflet of the bilayer by nonendocytic pathways, and for the times studied, the drug molecule remains trapped inside the pristine tube while remaining attached at the end of polystyrene-modified tube. On the other hand, carboxyl-terminated polystyrene functionalization allows the drug to be completely released into the lower leaflet of the bilayer without imposing damage to the membrane. This study shows that polystyrene functionalization is a promising alternative and facilitates drug delivery as a benchmark case.

Behavior of Citrate-Capped Ultrasmall Gold Nanoparticles on a Supported Lipid Bilayer Interface at Atomic Resolution

Nanomaterials have the potential to transform biological and biomedical research, with applications ranging from drug delivery and diagnostics to targeted interference of specific biological processes. Most existing research is aimed at developing nanomaterials for specific tasks such as enhanced biocellular internalization. However, fundamental aspects of the interactions between nanomaterials and biological systems, in particular, membranes, remain poorly understood. In this study, we provide detailed insights into the molecular mechanisms governing the interaction and evolution of one of the most common synthetic nanomaterials in contact with model phospholipid membranes. Using a combination of atomic force microscopy (AFM) and molecular dynamics (MD) simulations, we elucidate the precise mechanisms by which citrate-capped 5 nm gold nanoparticles (AuNPs) interact with supported lipid bilayers (SLBs) of pure fluid (DOPC) and pure gel-phase (DPPC) phospholipids. On fluid-phase DOPC membranes, the AuNPs adsorb and are progressively internalized as the citrate capping of the NPs is displaced by the surrounding lipids. AuNPs also interact with gel-phase DPPC membranes where they partially embed into the outer leaflet, locally disturbing the lipid organization. In both systems, the AuNPs cause holistic perturbations throughout the bilayers. AFM shows that the lateral diffusion of the particles is several orders of magnitude smaller than that of the lipid molecules, which creates some temporary scarring of the membrane surface. Our results reveal how functionalized AuNPs interact with differing biological membranes with mechanisms that could also have implications for cooperative membrane effects with other molecules.

Adsorption Dynamics of Surface-Modified Silica Nanoparticles at Solid-Liquid Interfaces

Understanding the adsorption dynamics of nanoparticles at solid-liquid interfaces is of paramount importance to engineer nanoparticles for a variety of applications. The nanoparticle surface chemistry is significant for controlling the adsorption dynamics. This study aimed to experimentally examine the adsorption of surface-modified round-shaped silica nanoparticles (with an average diameter of 12 nm), grafted with hydrophobic (propyl chains) and/or hydrophilic (polyethylene glycol chains) agents, at an aqueous solution-silica interface with spherical soda-lime glass beads (diameter of 3 mm) being used as adsorbents. While no measurable adsorption was observed for solely hydrophobic or hydrophilic nanoparticles, a considerable level of adsorption was detected for nanoparticles comprising both hydrophobic and hydrophilic agents. Various kinetic models were employed to model the adsorption dynamics of the responsive nanoparticles. The results demonstrated that the mixed diffusion-kinetics models could predict the dynamics better than the adsorption diffusion models, indicating that the dynamics is controlled by a combination of liquid film diffusion, intra-particle diffusion, and mass action. Additionally, the adsorption of the surface-modified silica nanoparticles onto a mineral silica surface was examined using molecular dynamics simulations. The interaction energy for nanoparticles comprising both hydrophobic and hydrophilic agents was evaluated to be more favorable than that of solely hydrophobic or hydrophilic nanoparticles.

CHARMM-GUI Implicit Solvent Modeler for Various Generalized Born Models in Different Simulation Programs

Implicit solvent models are widely used because they are advantageous to speed up simulations by drastically decreasing the number of solvent degrees of freedom, which allows one to achieve long simulation time scales for large system sizes. CHARMM-GUI, a web-based platform, has been developed to support the setup of complex multicomponent molecular systems and prepare input files. This study describes an Implicit Solvent Modeler (ISM) in CHARMM-GUI for various generalized Born (GB) implicit solvent simulations in different molecular dynamics programs such as AMBER, CHARMM, GENESIS, NAMD, OpenMM, and Tinker. The GB models available in ISM include GB-HCT, GB-OBC, GB-neck, GBMV, and GBSW with the CHARMM and Amber force fields for protein, DNA, RNA, glycan, and ligand systems. Using the system and input files generated by ISM, implicit solvent simulations of protein, DNA, and RNA systems produce similar results for different simulation packages with the same input information. Protein-ligand systems are also considered to further validate the systems and input files generated by ISM. Simple ligand root-mean-square deviation (RMSD) and molecular mechanics generalized Born surface area (MM/GBSA) calculations show that the performance of implicit simulations is better than docking and can be used for early stage ligand screening. These reasonable results indicate that ISM is a useful and reliable tool to provide various implicit solvent simulation applications.

MoS2 nanosheet induced destructive alterations in the Escherichia coli bacterial membrane

Two dimensional molybdenum disulfide (MoS₂) nanosheets have recently gained wide recognition for their efficient broad-spectrum antibacterial activity complemented with great biocompatibility and minimal bacterial resistance inducing capabilities. However, despite the numerous investigations, the molecular level interactions at the nano-bio interface responsible for their bactericidal activity remain obscure. Herein, through an atomistic molecular dynamics study, we attempt to seek an in-depth understanding of the atomic level details of the underlying mechanism of their antibacterial action against the Escherichia coli (E. coli) bacterial membrane. Our study reveals a two-step MoS₂ nanosheet interaction pathway with the bacterial membrane. The nanosheets spontaneously adhere to the membrane surface and prompt vigorous phospholipid extraction majorly via strong van der Waals interactions with lipid hydrophobic tails. The lipid extraction process originates a significant water intrusion in the bilayer hydrophobic region, signifying the onset of cytoplasmic leakage under realistic conditions. Further, a synergistic effect of lipid-lipid self-interactions and lipid-MoS₂ dispersion interactions drags the nanosheet to completely immerse in the bilayer hydrophobic core. The embedded nanosheets induce a layerwise structural rearrangement of the membrane lipids in their vicinity, thus altering the structural and dynamic features of the membrane in a localized manner by (i) increasing the lipid fatty acyl tail ordering and (ii) alleviating the lipid lateral dynamics. The detrimental efficacy of the nanosheets can be magnified by enlarging the nanosheet size or by increasing the nanosheet concentration. Our study concludes that the MoS₂ nanosheets can exhibit their antibacterial action through destructive phospholipid extraction as well as by altering the morphology of the membrane by embedding in the membrane core.

Development and characterization of chlorophyll-amended montmorillonite clays for the adsorption and detoxification of benzene

After disasters, such as forest fires and oil spills, high levels of benzene (> 1 ppm) can be detected in the water, soil, and air surrounding the disaster site, which poses a significant health risk to human, animal, and plant populations in the area. While remediation methods with activated carbons have been employed, these strategies are limited in their effectiveness due to benzene's inherent stability and limited retention to most surfaces. To address this problem, calcium and sodium montmorillonite clays were amended with a mixture of chlorophyll (a) and (b); their binding profile and ability to detoxify benzene were characterized using in vitro, in silico, and well-established ecotoxicological (ecotox) bioassay methods. The results of in vitro isothermal analyses indicated that chlorophyll-amended clays showed an improved binding profile in terms of an increased binding affinity (Kf = 668 vs 67), increased binding percentage (52% vs 11%), and decreased rates of desorption (28% vs 100%), compared to the parent clay. In silico simulation studies elucidated the adsorption mechanism and validated that the addition of the chlorophyll to the clays increased the adsorption of benzene through Van der Waals forces (i.e., aromatic π-π stacking and alkyl-π interactions). The sorbents were also assessed for their safety and ability to protect sensitive ecotox organisms (Lemna minor and Caenorhabditis elegans) from the toxicity of benzene. The inclusion of chlorophyll-amended clays in the culture medium significantly reduced benzene toxicity to both organisms, protecting C. elegans by 98-100% from benzene-induced mortality and enhancing the growth rates of L. minor. Isothermal analyses, in silico modeling, and independent bioassays all validated our proof of concept that benzene can be sequestered, tightly bound, and stabilized by chlorophyll-amended montmorillonite clays. These novel sorbents can be utilized during disasters and emergencies to decrease unintentional exposures from contaminated water, soil, and air.

Zwitterionic Osmolytes Revive Surface Charges under Salt Stress via Dual Mechanisms

To counter the stress of a salt imbalance, the cell often produces low molecular weight osmolytes to resuscitate homeostasis. However, how zwitterionic osmolytes would tune the electrostatic interactions among charged biomacromolecular surfaces under salt stress has eluded mainstream investigations. Here, via combination of molecular simulation and experiment, we demonstrate that a set of zwitterionic osmolytes is able to restore the electrostatic interaction between two negatively charged surfaces that had been masked in the presence of salt. Interestingly, the mechanisms of resurrecting charge interaction under excess salt are revealed to be mutually divergent and osmolyte specific. In particular, glycine is found to competitively desorb the salt ions from the surface via its direct interaction with the surface. On the contrary, TMAO and betaine counteract salt stress by retaining adsorbed cations but partially neutralizing their charge density via ion-mediated interaction. These access to alternative modes of osmolytic actions would provide the cell the required flexibility in combating salt stress.