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At least 541 records · Page 30

Extreme Metastability of Diamond and its Transformation to the BC8 Post-Diamond Phase of Carbon

Diamond possesses exceptional physical properties due to its remarkably strong carbon–carbon bonding, leading to significant resilience to structural transformations at very high pressures and temperatures. Despite several experimental attempts, synthesis and recovery of the theoretically predicted post-diamond BC8 phase remains elusive. Through quantum-accurate multimillion atom molecular dynamics (MD) simulations, we have uncovered the extreme metastability of diamond at very high pressures, significantly exceeding its range of thermodynamic stability. We predict the post-diamond BC8 phase to be experimentally accessible only within a narrow high pressure–temperature region of the carbon phase diagram. The diamond to BC8 transformation proceeds through premelting followed by BC8 nucleation and growth in the metastable carbon liquid. Here we propose a double-shock compression pathway for BC8 synthesis, which is currently being explored in experiments at the National Ignition Facility.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Molecular Picture of the Transient Nature of Lipid Rafts

In biological membranes, lipid rafts are now thought to be transient and nanoscopic. However, the mechanism responsible for these nanoscopic assemblies remains poorly understood, even in the case of model membranes. Therefore, it has proven extremely challenging to probe the physicochemical properties of lipid rafts at the molecular level. Here, we use all-atom molecular dynamics (MD) simulations and inelastic X-ray scattering (IXS), an intrinsically nanoscale technique, to directly probe the energy transfer and collective short-wavelength dynamics (phonons) of biologically relevant model membranes. We show that the nanoscale propagation of stress in lipid rafts takes place in the form of collective motions made up of longitudinal (compression waves) and transverse (shear waves) molecular vibrations. Importantly, we provide a molecular picture for the so-called van der Waals mediated "force from lipid" [Anishkin, A. et al. Proc. Natl. Acad. Sci. U.S.A. 2014, 111, 7898], a key parameter for the ionic channel mechano-transduction and the mechanism for the lipid transfer of molecular level stress [Aponte-Santamaría, C. et al. J. Am. Chem. Soc. 2017, 139, 13588]. Specifically, we describe how lipid rafts are formed and maintained through the propagation of molecular stress, lipid raft rattling dynamics, and a relaxation process. Eventually, the rafts dissipate through the self-diffusion of lipids making up the rafts. We also show that the molecular stress and viscoelastic properties of transient lipid rafts can be modulated through the use of hydrophobic biomolecules such as melatonin and tryptophan. Overall, the herein proposed mechanism describing the molecular interactions for the formation and dissolution of lipid rafts may offer insights as to how lipid rafts enable biological function.

36 MATERIALS SCIENCE↗

Quantification of Mono- and Multivalent Counterion-Mediated Bridging in Polyelectrolyte Brushes

Multivalent counterion-induced bridging interactions have been identified as the key mechanism of drastic collapse of the height of polyelectrolyte (PE) brushes. In this article, we employ all-atom molecular dynamics (MD) simulations to quantify the bridging interactions in PE brushes for counterions of different sizes and valences. We identify that unlike the current notion, bridging interactions are not the sole function of the counterion valence. Rather the bridging interactions depend on the fraction of counterions (of a given type) that get physically condensed on the PE backbone as well as the size of the counterion solvation shell. These mechanisms ensure that certain monovalent counterions demonstrate much stronger bridging interactions than that witnessed for certain divalent and trivalent counterions, while certain counterions of identical valences show drastically different bridging. Here, we argue that these counterion-specific bridging interactions eventually enable not only the significant reduction of the PE brush height in presence of certain multivalent screening counterions, but may also give rise to scenarios where the brush height reduction for certain monovalent counterions is larger than certain divalent and trivalent counterions. This latter observation contradicts the experimental findings where the multivalent counterions invariably led to a larger decrease in the height of the PE brushes: we argue that this discrepancy stems from the fact that in our simulations we only consider densely grafted and short (and hence less flexible) PE brushes that hinder the formation of different laterally inhomogeneous structures (like pinned micelles and cylindrical bundles) that would have led to a larger brush height reduction (in experiments, which invariably consider longer and less densely grafted brushes, the formation of such inhomogeneous structures are primarily responsible for larger brush height reduction in presence of multivalent counterions). Finally, we also probe the dynamic properties of the counterions (i.e., their time-dependent displacements) and their bridging interactions (i.e., lifetime of bridging interactions).

42 ENGINEERING↗

Subdiffusive High-Pressure Hydrogen Gas Dynamics in Elastomers

We report elastomeric rubber materials serve a vital role as sealing materials in the hydrogen storage and transport infrastructure. With applications including O-rings and hose liners, these components are exposed to pressurized hydrogen at a range of temperatures, cycling rates, and pressure extremes. High-pressure exposure and subsequent rapid decompression often lead to cavitation and stress-induced damage of the elastomer due to localization of the hydrogen gas. Here, we use all-atom classical molecular dynamics simulations to assess the impact of compositional variations on gas diffusion within the commonly used elastomer ethylene–propylene–diene monomer (EPDM). With the aim to build a predictive understanding of precursors to cavitation and to motivate material formulations that are less sensitive to hydrogen-induced failure, we perform systematic simulations of gas dynamics in EPDM as a function of temperature, gas concentration, and cross-link density. Our simulations reveal anomalous, subdiffusive hydrogen motion at pressure and intermediate times. We identify two groups of gas with different mobilities: one group exhibiting high mobility and one group exhibiting low mobility due to their motion being impeded by the polymer. With decreasing temperatures, the low-mobility group shows increased gas localization, the necessary precursor for cavitation damage in these materials. At lower temperatures, increasing cross-link density led to greater hydrogen gas mobility and a lower fraction of caged hydrogen, indicating that increasing cross-link density may reduce precursors to cavitation. Finally, we use a two-state kinetic model to determine the energetics associated with transitions between these two mobility states.

36 MATERIALS SCIENCE↗

Charge-Density-Specific Response of Grafted Polyelectrolytes to Electric Fields: Bending or Tilting?

The response of polyelectrolytes (PEs) to applied electric fields drive applications in energetics, diagnostics, materials development, and many more. Here we employ all-atom molecular dynamics (MD) simulations to probe the response of grafted PE brushes to axial electric fields. For PEs with large charge densities, the electric field triggers a left-right asymmetric distribution of counterions around the PE backbone: consequently, depending on the location (left or right), there is an unequal screening and an unequal force on the PE functional groups causing a bending-driven brush height reduction. However, for the weakly charged PEs, the electric field causes a uniform distribution of the counterions across the brush enforcing a uniform (without left-right asymmetry) partially unscreened PE brush: therefore, all the brush segments experience similar force causing a brush tilting-driven brush height reduction. As a result, such bending versus tilting responses is commensurate with the electric-field-driven increase (decrease) in the flexibility of strongly (weakly) charged PEs.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Combined Machine Learning and Molecular Dynamics Reveal Two States of Hydration of a Single Functional Group of Cationic Polymeric Brushes

The state of hydration of a macromolecular system regulates a plethora of different properties of such a system. In this article, we develop a novel machine learning (ML) approach, based on the unsupervised clustering algorithm, for probing the hydration behavior of the {N(CH 3 ) 3 } + functional group of the PMETAC [Poly(2-(methacryloyloxy)ethyl trimethylammonium chloride] polyelectrolyte (PE) brush system. The PE brushes and the brush-supported water molecules and counterions (chloride ions) are first described using all-atom molecular dynamics (MD) simulations. The simulation data is subsequently used in our ML framework to identify that (1) the {N(CH 3 ) 3 } + functional groups of the PMETAC brushes have two distinct hydration states with one state (state 1) being characterized by less structured water molecules and the other state (state 2) being characterized by more structured water molecules and (2) an enhancement in the brush grafting density leads to the progressive dissapparenace of state 2. An increase in the grafting density increases the number of chloride counterions in a given volume around the {N(CH 3 ) 3 } + functional group and increases the number of shared water molecules between the {N(CH 3 ) 3 } + and Cl - . The chloride counterions are associated with a hydration layer with much less structured water molecules. Therefore, with an increase in the grafting density, an increase in the percentage of shared water molecules leads to the prevalence of the hydration state [of the {N(CH 3 ) 3 } + moiety] with less structured water molecules. Finally, we explain how the present findings are commensurate with two key previous related results, namely a significantly large chloride ion mobility inside the PMETAC brush layer and the {N(CH 3 ) 3 } + -Cl - average distance remaining independent of the PMETAC brush grafting density. Furthermore, we anticipate that the combined ML-MD-simulation approach proposed in this study can be adapted to probe other soft matter systems to reveal new insights of the underlying mechanisms of emergent phenomenon.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Hydration and Restructuring of Polar Polymer Interfaces: Implications in Antifouling and Responsive Materials

Manipulating polymer interfaces is crucial for understanding how structure influences function in applications spanning biofouling prevention to energy storage. Moreover, observing how polymers adapt their microscopic structure to changes in their local environment can reveal essential properties that govern their performance in such applications, providing key insights into how to design more effective interfaces. Here, in this study, a series of “grafting-from” polymer brushes with side chains varying in charge, are probed by sum frequency generation (SFG) and modeled using all-atom molecular dynamics (MD) simulations to elucidate how chemical makeup and charge mediate interfacial restructuring in dry versus hydrated states. Results show that charge, in progressing from nonpolar to cationic to zwitterionic, results in dramatic changes in interfacial structure and overall hydration. While net neutral systems, regardless of bulk phase polarity, show minimal interfacial water structuring, the cationic species exhibits strong bulk water signals from the surface potential. Meanwhile, the polymer brushes themselves restructure in water differently independent of charge, impacting the functional groups that are presented to the aqueous phase. Nonpolar and cationic species for instance undergo a change in alkyl group orientations to accommodate hydrating water molecules, whereas the zwitterionic polymer becomes completely disordered in water. Overall, the structure-based behavior trends presented herein have implications in antifouling applications and responsive material interfaces.

biointerface↗

Antielectrophoretic Response-Driven Bending–Tilting Deformation of Cationic Polyelectrolyte Brushes Drives Nonlinear Electroosmotic Transport in Brush-Grafted Nanochannels

In this paper, we use all-atom molecular dynamics (MD) simulations to describe a non-linearly enhanced electroosmotic (EOS) flow, where, in a nanochannel grafted with cationic PMETAC ([Poly(2-(Methacryloyloxy)Ethyl) Trimethylammonium Chloride]) brushes, a two-fold increase in the electric field strength leads to a several-fold (more than two-fold) increase in the EOS flow strength and volume flow rate. The electric field enforces the PMETAC brushes to undergo a bending-tilting driven deformation with a significant portion of the brush layer becoming parallel to the grafting surface. In response, a substantial fraction of the counterions leave the brush layer (hence become more mobile), but instead of going into the bulk, accumulate at the brush-bulk interface, i.e., stay in proximity of the brush segments aligned parallel to the grafting surface. This creates an interesting situation, where the counterions are not completely within the brush layer, yet they fully screen the brush charges. Such “freer” conditions enable the counterions to achieve very high velocity, thereby ensuring that the water solvating the counterions themselves move very fast triggering the significantly augmented EOS transport. Probing deeper we can identify that the bending-tilting driven brush deformation, enforcing the brushes to align parallel to the substrate, results from the anti-electrophoretic behavior of the brushes, where despite being positively charged, the brushes move against the electric field direction. Such an anti-electrophoretic behavior of the PE brushes, which has not been reported before, can be associated with the very fast velocities of the negatively charged counterions and the electrostatic and hydrodynamic coupling of the counterions with the positive functional groups of the brushes. Here, we anticipate that the findings of this paper will shed light on strategies for nanochannel flow, the anti-electrophoretic response of charged polymer chains, and the significance of capturing the detailed chemical architecture of polyelectrolytes in nanoscale science and engineering.

36 MATERIALS SCIENCE↗

Selective and Stable Ethanol Synthesis via Electrochemical CO 2 Reduction in a Solid Electrolyte Reactor

Electrochemical CO 2 reduction to ethanol faces challenges such as low selectivity, a product mixture with liquid electrolyte, and poor catalyst/reactor stability. Here, we developed a grain-rich zinc-doped Cu 2 O precatalyst that presented a high ethanol Faradaic efficiency of over 40% under a current density of 350 mA·cm –2 . Our density functional theory (DFT) simulation suggested that Zn atoms inside the structure have a greater carbophilicity than the Cu atoms to help facilitate *CHCHO formation, a key reaction intermediate toward ethanol instead of other C 2 products. Here, a high Faradaic efficiency ratio between ethanol and ethylene (FE EtOH /FE C2H4 ) reached 2.34 in the zinc-doped Cu 2 O precatalyst, representing an over 4-fold improvement compared to bare Cu 2 O precatalyst. By integrating this Cu-based catalyst into a porous solid electrolyte (PSE) reactor with a salt-managing design, we achieved stable ethanol production for over 180 h under a current density of 250 mA·cm –2 while maintaining ethanol selectivity at ~30%.

09 BIOMASS FUELS↗

Simultaneous Energy Generation and Flow Enhancement (Electroslippage Effect) in Polyelectrolyte Brush Functionalized Nanochannels

Energy generation through nanofluidics is a topic of great nanotechnological relevance. In this work, we conduct all-atom molecular dynamics (MD) simulations of the transport of water and ions in a pressure-driven flow in nanochannels grafted with charged polyelectrolyte (PE) brushes and discover the possibility of simultaneous electrokinetic energy generation and flow enhancement (henceforth denoted as the electroslippage effect). Such PE-brush-functionalized nanochannels have been recently shown to demonstrate an overscreening (OS) effect (characterized by the presence of a greater number of screening counterions within the PE brush layer than needed to screen the PE brush charges), a consequent presence of excess coions within the PE brush-free bulk, and a coion-driven electroosmotic (EOS) transport in the presence of small to moderate applied axial electric fields. Here, however, we find that the streaming current, which represents the current generated by the flow-driven downstream advection of the charge imbalance present within the electric double layer (EDL) that screen the PE brush charges, is governed by the migration of the counterions. This stems from the fact that the highest contribution to the overall streaming current arises from the region near the PE brush-water interface (where there is an excess of counterions), while the brush-free bulk yields a hitherto unreported, but small, coion-dictated streaming current. This downstream advection of the charge imbalance (and the resultant counterion-driven streaming current) eventually leads to the development of an electric field (streaming electric field) in the direction that is opposite to the direction of the counterion-driven streaming current. The streaming current and the streaming electric field interact to generate the electrokinetic energy. Equally importantly, this streaming electric field induces an EOS transport, which becomes coion-driven, due to the presence of excess coions in the brush-free bulk. For the case of nanochannels grafted with negatively charged PE brushes, the streaming electric field will be in a direction that is opposite to the pressure-driven transport, and hence the coion (or anion) driven EOS flow, will be in the same direction as the pressure-driven transport. On the other hand, for the case of nanochannels grafted with positively charged PE brushes, the streaming electric field will be in the same direction as the pressure-driven flow, and hence the coion (or cation) driven EOS flow, will again be in the same direction as the pressure-driven flow. Therefore, whenever there occurs the presence of the OS and the resulting coion-driven EOS transport in PE brush grafted nanochannels, regardless of the sign of the charges of the PE brushes, this EOS transport will always aid the pressure-driven transport and will cause the most fascinating increase in the net volume flow rate across the nanochannel cross section, which is the electroslippage effect.

overscreening↗

Ethanol-Induced Condensation and Decondensation in DNA-Linked Nanoparticles: A Nucleosome-like Model for the Condensed State

Inspired by the conventional use of ethanol to induce DNA precipitation, ethanol condensation has been applied as a routine method to dynamically tune “bond” lengths (i.e., the surface-to-surface distances between adjacent nanoparticles that are linked by DNA) and thermal stabilities of colloidal crystals involving DNA-linked nanoparticles. However, the underlying mechanism of how the DNA bond that links gold nanoparticles changes in this class of colloidal crystals in response to ethanol remains unclear. Here, we conducted a series of all-atom molecular dynamic (MD) simulations to explore the free energy landscape for DNA condensation and decondensation. Our simulations confirm that DNA condensation is energetically much more favorable under 80% ethanol conditions than in pure water, as a result of ethanol’s role in enhancing electrostatic interactions between oppositely charged species. Moreover, the condensed DNA adopts B-form in pure water and A-form in 80% ethanol, which indicates that the higher-order transition does not affect DNA’s conformational preferences. We further propose a nucleosome-like supercoiled model for the DNA condensed state, and we show that the DNA end-to-end distance derived from this model matches the experimentally measured DNA bond length of about 3 nm in the fully condensed state for DNA where the measured length is 16 nm in water. Altogether, this study provides an atomistic understanding of the mechanism underlying ethanol-induced condensation and water-induced decondensation, while our proposed nucleosome-like model allows the design of new strategies for interpreting experimental studies of DNA condensation.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Computational alchemy clarifies origins of alloy strengthening

Solid solution strengthening (SSS) is widely used to enhance mechanical properties of metals. Originally developed for dilute alloys, classical SSS theories are presently challenged by the rise of complex concentrated alloys (CCA) with nearly equiatomic compositions. Here, we propose and develop a method of “computational alchemy” in which interatomic interactions are modified to systematically vary two key physical parameters defining SSS - atomic size misfit and elastic stiffness misfit - over a maximally wide range of two misfits. The resulting alchemical alloys are subjected to massive (~10 8 atoms) molecular dynamics (MD) simulations reproducing full complexity of plastic strength response. At variance with prevailing views, stiffness misfit is observed to contribute to SSS on par if not more than size misfit. Furthermore, depending on exactly how two misfits are combined, they result in synergistic (amplification) or antagonistic (compensation) effect on alloy strengthening. Unlike real CCAs in which each component element comes with its own specific size and stiffness, our alchemical model alloys span the space of two misfits continuously revealing trends in alloy strengthening unrecognized so far. Our study demonstrates unique value of intentionally unrealistic models for gaining deep physical insights into material behaviors that are difficult to reveal otherwise.

36 MATERIALS SCIENCE↗

Carbon nanotube porin diffusion in mixed composition supported lipid bilayers

Carbon nanotube porins (CNTPs), short pieces of carbon nanotubes capable of self-inserting into a lipid bilayer, represent a simplified model of biological membrane channels. We have used high-speed atomic force microscopy (HS-AFM) and all-atom molecular dynamics (MD) simulations to study the behavior of CNTPs in a mixed lipid membrane consisting of DOPC lipid with a variable percentage of DMPC lipid added to it. HS-AFM data reveal that the CNTPs undergo diffusive motion in the bilayer plane. Motion trajectories extracted from the HS-AFM movies indicate that CNTPs exhibit diffusion coefficient values broadly similar to values reported for membrane proteins in supported lipid bilayers. The data also indicate that increasing the percentage of DMPC leads to a marked slowing of CNTP diffusion. MD simulations reveal a CNTP-lipid assembly that diffuses in the membrane and show trends that are consistent with the experimental observations.

77 NANOSCIENCE AND NANOTECHNOLOGY↗

The allosteric mechanism leading to an open-groove lipid conductive state of the TMEM16F scramblase

TMEM16F is a Ca 2+ -activated phospholipid scramblase in the TMEM16 family of membrane proteins. Unlike other TMEM16s exhibiting a membrane-exposed hydrophilic groove that serves as a translocation pathway for lipids, the experimentally determined structures of TMEM16F shows the groove in a closed conformation even under conditions of maximal scramblase activity. It is currently unknown if/how TMEM16F groove can open for lipid scrambling. Here we describe the analysis of ~400 µs all-atom molecular dynamics (MD) simulations of the TMEM16F revealing an allosteric mechanism leading to an open-groove, lipid scrambling competent state of the protein. The groove opens into a continuous hydrophilic conduit that is highly similar in structure to that seen in other activated scramblases. The allosteric pathway connects this opening to an observed destabilization of the Ca 2+ ion bound at the distal site near the dimer interface, to the dynamics of specific protein regions that produces the open-groove state to scramble phospholipids.

59 BASIC BIOLOGICAL SCIENCES↗

Atomic-scale control of tunneling in donor-based devices

Atomically precise donor-based quantum devices are a promising candidate for solid-state quantum computing and analog quantum simulations. However, critical challenges in atomically precise fabrication have meant systematic, atomic scale control of the tunneling rates and tunnel coupling has not been demonstrated. Here using a room temperature grown locking layer and precise control over the entire fabrication process, we reduce unintentional dopant movement while achieving high quality epitaxy in scanning tunnelling microscope (STM)-patterned devices. Using the Si(100)2 × 1 surface reconstruction as an atomically-precise ruler to characterize the tunnel gap in precision-patterned single electron transistors, we demonstrate the exponential scaling of the tunneling resistance on the tunnel gap as it is varied from 7 dimer rows to 16 dimer rows. We demonstrate the capability to reproducibly pattern devices with atomic precision and a donor-based fabrication process where atomic scale changes in the patterned tunnel gap result in the expected changes in the tunneling rates.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Graphene-extracted membrane lipids facilitate the activation of integrin α v β 8

Despite the remarkable electrochemical properties of graphene, strong van der Waals attraction between graphene and biomolecules often causes cytotoxicity, which hinders its applications in the biomedical field. Unfortunately, surface passivation of graphene might stimulate undesired immune response as the nanomaterial triggers cytokine production through membrane receptor activation. In this work, we use all-atom Molecular Dynamics (MD) simulations to unravel the underlying mechanism of graphene-induced inside-out activation of integrin αvβ8, a prominent membrane receptor expressed in immune cells. We model the transmembrane (TM) domains of integrin αvβ8 in a 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) lipid bilayer and observe the structural changes in the integrin–membrane complex when interacting with a graphene nanosheet across the membrane. We find that the β8 TM domain interacts with the graphene nanosheet directly or indirectly through extracted lipids, facilitating the pulling of a β8 subunit away from an αv subunit and thus leading to the disruption of the TM domain association by breaking the hydrophobic cluster in the cytoplasmic domains of the αv and β8 subunits. Alanine substitution of two conserved phenylalanine residues on the αv subunit at this hydrophobic cluster further reveals the importance of a stable T-shaped structure in retaining integrin in its inactive state. Our results agree with previous studies on the interactions between other integrin subtypes and their endogenous activators, suggesting an intriguing role that the graphene nanosheet may play in the integrin-related signal transduction during its interaction with the membrane.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Bond clusters control rupture force limit in shear loaded histidine-Ni 2+ metal-coordinated proteins

Dynamic noncovalent interactions are pivotal to the structure and function of biological proteins and have been used in bioinspired materials for similar roles. Metal-coordination bonds, in particular, are especially tunable and enable control over static and dynamic properties when incorporated into synthetic materials. Despite growing efforts to engineer metal-coordination bonds to produce strong, tough, and self-healing materials, the systematic characterization of the exact contribution of these bonds towards mechanical strength and the effect of geometric arrangements is missing, limiting the full design potential of these bonds. In this work, we engineer the cooperative rupture of metal-coordination bonds to increase the rupture strength of metal-coordinated peptide dimers. Utilizing all-atom steered molecular dynamics simulations on idealized bidentate histidine-Ni 2+ coordinated peptides, we show that histidine-Ni 2+ bonds can rupture cooperatively in groups of two to three bonds. We find that there is a strength limit, where adding additional coordination bonds does not contribute to the additional increase in the protein rupture strength, likely due to the highly heterogeneous rupture behavior exhibited by the coordination bonds. Further, we show that this coordination bond limit is also found natural metal-coordinated biological proteins. Using these insights, we quantitatively suggest how other proteins can be rationally designed with dynamic noncovalent interactions to exhibit cooperative bond breaking behavior. Altogether, this work provides a quantitative analysis of the cooperativity and intrinsic strength limit for metal-coordination bonds with the aim of advancing clear guiding molecular principles for the mechanical design of metal-coordinated materials.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗