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Although the carbon nanotube (CNT) features superior thermal properties in its pristine form, the chemical functionalization often required for many applications of CNT inevitably degrades the structural integrity and affects the transport of energy carriers. In this article, the effect of the side wall functionalization on the phonon energy transmission along the symmetry axis of CNT is studied using the phonon wave packet method. Three different functional groups are studied: methyl (-CH3), vinyl (-C2H3), and carboxyl (-COOH). We find that, near Γ point of the Brillouin zone, acoustic phonons show ideal transmission, while the transmission of the optical phonons is strongly suppressed. A positive correlation between the energy transmission coefficient and the phonon group velocity is observed for both acoustic and optical phonon modes. On comparing the transmission due to functional groups with equivalent point mass defects on CNT, we find that the chemistry of the functional group, rather than its molecular mass, has a dominant role in determining phonon scattering, hence the transmission, at the defect sites. [ABSTRACT FROM AUTHOR]

This article explores the behavior of interface thermal conductance of longitudinally connected (6,6) nanotubes-connected through CH2 linkages-using nonequilibrium molecular dynamics (NEMD) and wave packet simulations. Here, we study the effect of connected linkers on the interface thermal conductance and thermal energy transmission coefficients for several phonon modes. Our simulation results suggest that interface thermal conductance between nanotubes strongly depends on the number of CH2 linkers. The more the number of CH2 linkers, the higher the conductance. Further insights into phonon energy transmission are provided from wave packet simulations. Here, we find that the behavior of transmission for various studied acoustic and optical phonon modes is complex in nature, where the thermal transmission coefficients do not always correlate with number of CH2 linkages. However, when the contributions from all the modes are added together, the overall interface thermal conductance agrees well with NEMD simulations. [ABSTRACT FROM AUTHOR]

A coarse-grained computer simulation model is used to study the immobilization of a dynamic tethered membrane (representation of a clay platelet) in a matrix of mobile peptide chains CR3-1:1Trp[Single_Bond]2Pro[Single_Bond]3Ser[Single_Bond]4Ser[Single_Bond]5Tyr[Single_Bond]6Leu[Single_Bond]7Ser[Single_Bond]8Pro[Single_Bond]9Ile[Single_Bond]10Pro[Single_Bond]11Tyr[Single_Bond]12Ser and S2:1His[Single_Bond]2Gly[Single_Bond]3Ile[Single_Bond]4Asn[Single_Bond]5Thr[Single_Bond]6Thr[Single_Bond]7Lys[Single_Bond]8Pro[Single_Bond]9Phe[Single_Bond]10Lys[Single_Bond]11Ser[Single_Bond]12Val on a cubic lattice. Each residue interacts with the membrane nodes with appropriate interaction and executes their stochastic motion with the Metropolis algorithm. Density profiles, binding energy of each residue, mobility, and targeted structural profile are analyzed as a function of peptide concentration. We find that the binding of peptides S2 is anchored by lysine residues (7Lys,10Lys) while peptides CR3-1 do not bind to membrane. The membrane slows down as peptides (S2) continues to bind leading to its eventual pinning. How fast the immobilization of the membrane occurs depends on peptide concentration. Binding of peptide (S2) modulates the morphology of the membrane. The immobilization of membrane occurs faster if peptides (S2) are replaced by the homopolymer of lysine ([Lys]12 of the same molecular weight), the strongest binding residue. The surface of membrane can be patterned with somewhat reduced roughness with the homopolymer of lysine than that with peptide (S2). [ABSTRACT FROM AUTHOR]

Presents a study that observed Curie transition in vanadium-fluorine-terbium-Iron random copolymer of fixed chemical composition has been investigated as a function of processing history. Analysis of the solution cast and melt crystallized materials using differential scanning calorimetry and wide angle x-ray diffraction; Thermal analysis; Wide angle x-ray diffraction.

In order to understand how oxidation rate of graphene surfaces affects single-stranded poly-thymine, poly(T)20, structure during physisorption, all-atom molecular dynamics simulations are performed. In aqueous solutions, poly(T)20 is a complex structure with stacked and coiled regions. However, on the graphene surfaces, there are three different regimes for the adsorption process, which heavily depends on the surface oxidation: (1) on pristine graphene or graphene oxide (GO) with low oxygen coverage (GO 5%) the stacked poly(T)20 structure becomes unfolded due to formation of strong π-π interactions with the surface, (2) on graphene oxide with moderate oxygen coverage (GO 10%-25%) the structure of poly(T)20 is well preserved because of the balance between van der Waals and electrostatic interactions, and (3) on graphene oxide with high oxygen content (GO 30%-60%) stacked poly(T)20 structure is locally disrupted due to formation of strong hydrogen bonds with the surface. Moreover, surface roughness due to the presence of oxygen groups plays a pivotal role in structural retention of poly(T)20 by preventing its nucleobases from forming π-π stacking interactions with the surface. [ABSTRACT FROM AUTHOR]

Recognition and manipulation of graphene edges enable the control of physical properties of graphene-based devices. Recently, the authors have identified a peptide that preferentially binds to graphene edges from a combinatorial peptide library. In this study, the authors examine the functional basis for the edge binding peptide using experimental and computational methods. The effect of amino acid substitution, sequence context, and solution pH value on the binding of the peptide to graphene has been investigated. The N-terminus glutamic acid residue plays a key role in recognizing and binding to graphene edges. The protonation, substitution, and positional context of the glutamic acid residue impact graphene edge-binding. Our findings provide insights into the binding mechanisms and the design of peptides for recognizing and functionalizing graphene edges. [ABSTRACT FROM AUTHOR]

In this work, we grow thin MoS2 films (50–150 nm) uniformly over large areas (＞1 cm2) with strong basal plane (002) or edge plane (100) orientations to characterize thermal anisotropy. Measurement results are correlated with molecular dynamics simulations of thermal transport for perfect and defective MoS2 crystals. The correlation between predicted (simulations) and measured (experimental) thermal conductivity are attributed to factors such as crystalline domain orientation and size, thereby demonstrating the importance of thermal boundary scattering in limiting thermal conductivity in nano-crystalline MoS2 thin films. Furthermore, we demonstrate that the cross-plane thermal conductivity of the films is strongly impacted by exposure to ambient humidity. [ABSTRACT FROM AUTHOR]

Interaction with the solvent plays a critical role in modulating the structure and dynamics of a protein. Because of the heterogeneity of the interaction strength, it is difficult to identify multi-scale structural response. Using a coarse-grained Monte Carlo approach, we study the structure and dynamics of a protein (H3.1) in effective solvent media. The structural response is examined as a function of the solvent-residue interaction strength (based on hydropathy index) in a range of temperatures (spanning low to high) involving a knowledge-based (Miyazawa-Jernigan(MJ)) residue-residue interaction. The protein relaxes rapidly from an initial random configuration into a quasi-static structure at low temperatures while it continues to diffuse at high temperatures with fluctuating conformation. The radius of gyration (Rg) of the protein responds non-monotonically to solvent interaction, i.e., on increasing the residue-solvent interaction strength (fs), the increase in Rg (fs≤fsc) is followed by decay (fs≥fsc) with a maximum at a characteristic value (fsc) of the interaction. Raising the temperature leads to wider spread of the distribution of the radius of gyration with higher magnitude of fsc. The effect of solvent on the multi-scale (λ: residue to Rg) structures of the protein is examined by analyzing the structure factor (S(q),|q| = 2π/λ is the wave vector of wavelength, λ) in detail. Random-coil to globular transition with temperature of unsolvated protein (H3.1) is dramatically altered by the solvent at low temperature while a systematic change in structure and scale is observed on increasing the temperature. The interaction energy profile of the residues is not sufficient to predict its mobility in the solvent. Fine-grain representation of protein with two-node and three-node residue enhances the structural resolution; results of the fine-grained simulations are consistent with the finding described above of the coarse-grained description with one-node residue. [ABSTRACT FROM AUTHOR]

A hierarchical computational approach (all-atom residue to all-residue peptide) is introduced to study self-organizing structures of peptides as a function of temperature. A simulated residue-residue interaction involving all-atom description, analogous to knowledge-based analysis (with different input), is used as an input to a phenomenological coarse-grained interaction for large scales computer simulations. A set of short peptides P1 (1H 2S 3S 4Y 5W 6Y 7A 8F 9N 10N 11K 12T) is considered as an example to illustrate the utility. We find that peptides assemble rather fast into globular aggregates at low temperatures and disperse as random-coil at high temperatures. The specificity of the mass distribution of the self-assembly depends on the temperature and spatial lengths which are identified from the scaling of the structure factor. Analysis of energy and mobility profiles, gyration radius of peptide, and radial distribution function of the assembly provide insight into the multi-scale (intra- and inter-chain) characteristics. Thermal response of the global assembly with the simulated residue-residue interaction is consistent with that of the knowledge-based analysis despite expected quantitative differences. [ABSTRACT FROM AUTHOR]

For the energy bandgap of semiconducting graphene nano mesh (GNM), chirality dependent scaling rules have been proposed so far. Based on extensive tight binding studies and simple geometric arguments, we report that Pedersen scaling governs not only the energy bandgap but also the effective mass of the Bloch electron of the semiconducting GNM regardless of its chirality or the crystallography of the mesh holes when the hole areal fraction is low. [ABSTRACT FROM AUTHOR]

The structure of a protein (H2AX) as a function of temperature is examined by three knowledge-based phenomenological interactions, MJ (Miyazawa and Jernigan), BT (Betancourt and Thirumalai), and BFKV (Bastolla et al.) to identify similarities and differences in results. Data from the BT and BFKV residue-residue interactions verify finding with the MJ interaction, i.e., the radius of gyration (Rg) of H2AX depends non-monotonically on temperature. The increase in Rg is followed by a decay on raising the temperature with a maximum at a characteristic value, Tc, which depends on the knowledge-based contact matrix, TcBFKV ≤ TcMJ ≤ TcBT. The range (ΔT) of non-monotonic thermal response and its decay pattern with the temperature are sensitive to interaction. A rather narrow temperature range of ΔTMJ ≈ 0.015–0.022 with the MJ interaction expands and shifts up to ΔTBT ≈ 0.018–0.30 at higher temperatures with the BT interaction and shifts down with the BFKV interaction to ΔTBFKV ≈ 0.011–0.018. The scaling of the structure factor with the wave vector reveals that the structure of the protein undergoes a transformation from a random coil at high temperature to a globular conformation at low temperatures. [ABSTRACT FROM AUTHOR]

The effect of temperature on the conformation of a histone (H3.1) is studied by a coarse-grained Monte Carlo simulation based on three knowledge-based contact potentials (MJ, BT, BFKV). Despite unique energy and mobility profiles of its residues, the histone H3.1 undergoes a systematic (possibly continuous) structural transition from a random coil to a globular conformation on reducing the temperature. The range over which such a systematic response in variation of the radius of gyration (Rg) with the temperature (T) occurs, however, depends on the potential, i.e. ΔTMJ ≈ 0.013-0.020, ΔTBT ≈ 0.018-0.026, and ΔTBFKV ≈ 0.006-0.013 (in reduced unit). Unlike MJ and BT potentials, results from the BFKV potential show an anomaly where the magnitude of Rg decreases on raising the temperature in a range ΔTA ≈ 0.015-0.018 before reaching its steady-state random coil configuration. Scaling of the structure factor, S(q) ∝ q-1/v, with the wave vector, q=2π/λ, and the wavelength, λ reveals a systematic change in the effective dimension (De~1/n) of the histone with all potentials (MJ, BT, BFKV): De~3 in the globular structure with De~2 for the random coil. Reproducibility of the general yet unique (monotonic) structural transition of the protein H3.1 with the temperature (in contrast to non-monotonic structural response of a similar but different protein H2AX) with three interaction sets shows that the knowledge-based contact potential is viable tool to investigate structural response of proteins. Caution should be exercise with the quantitative comparisons due to differences in transition regimes with these interactions. [ABSTRACT FROM AUTHOR]

Phonon scattering at the carbon nanotube-graphene interface is studied in the pillared graphene structure, using the phonon wave packet method. Qualitatively different scattering characteristics, compared to previous studies of carbon nanotube systems, are observed. The phonon group velocity, dictating the energy transmission in simple carbon nanotube systems, is found to play an insignificant role. Distributing the incoming phonon energy to both sides of the interface more or less equally, the graphene interface provides a strong diffusive scattering site, which features a microscopic understanding of the decisive role of junction on the thermal transport in the pillared graphene hierarchical structure. [ABSTRACT FROM AUTHOR]

Histone proteins are not only important due to their vital role in cellular processes such as DNA compaction, replication and repair but also show intriguing structural properties that might be exploited for bioengineering purposes such as the development of nano-materials. Based on their biological and technological implications, it is interesting to investigate the structural properties of proteins as a function of temperature. In this work, we study the spatial response dynamics of the histone H2AX, consisting of 143 residues, by a coarse-grained bond fluctuating model for a broad range of normalized temperatures. A knowledge-based interaction matrix is used as input for the residue-residue Lennard-Jones potential. We find a variety of equilibrium structures including global globular configurations at low normalized temperature (T*=0:014), combination of segmental globules and elongated chains (T*=0:016,0:017), predominantly elongated chains (T*=0:019,0:020), as well as universal SAW conformations at high normalized temperature (T*0:023). The radius of gyration of the protein exhibits a non-monotonic temperature dependence with a maximum at a characteristic temperature (T* c≥0:019) where a crossover occurs from a positive (stretching at T*≤T*c ) to negative (contraction at T*≤T* c ) thermal response on increasing T*. [ABSTRACT FROM AUTHOR]

Monte Carlo simulations are used to model the self-organizing behavior of the biomineralizing peptideKSL (KKVVFKVKFK) in the presence of phosphate. Originally identified as an antimicrobial peptide, KSL also directs the formation of biosilica through a hypothetical supramolecular template that requires phosphate for assembly. Specificity of each residue and the interactions between the peptide and phosphate are considered in a coarse-grained model. Both local and global physical quantities are calculated as the constituents execute their stochastic motion in the presence and absence of phosphate. Ordered peptide aggregates develop after simulations reach thermodynamic equilibrium, wherein phosphates form bridging ligands with lysines and are found interdigitated between peptide molecules. Results demonstrate that interactions between the lysines and phosphate drive self-organization into lower energy conformations of interconnected peptide scaffolds that resemble the supramolecular structures of polypeptide- and polyamine-mediated silica condensation systems. Furthermore, the specific phosphate–peptide organization appears to mimic the zwitterionic structure of native silaffins (scaffold proteins of diatom shells), suggesting a similar template organization for silica deposition between the in vitroKSL and silaffin systems. [ABSTRACT FROM AUTHOR]

The article discusses how computer simulation modeling can help predict the dispersal of different solvent matrices. Topics include a discussion regarding entropy dissipation, multiscale dynamics, and intercalation. An explanation of sheets, the basic constituents of sheets, and their usefulness to researchers are presented. Also presented is an in-depth examination of the transformation process from particles to sheet, coarse-grained models, and sheet conformation and dynamics.

Presents materials and components for scientific instruments and apparatus. Intelligent link; Noncontact milliammeter; Optical power meter; Moisture analysis; Pulse-delay generator; Optical mount; Lubricant; Phototherapy radiometer; Custom charge coupled devices; Miniature process manometer.

Features materials and components of various scientific instruments. Inclusion of Uvex Safety Inc.'s laser alignment models of the diffuse viewing only family of laser protective eyewear; AVTECH Electrosystems Ltd.'s Model AV-1023-C dual channel pulser; VALCOR Scientific's SV600 Series of High Purity, Solenoid Operated Dispensing/Metering Pumps.

Focuses on different scientific materials and components for use in physics research. Alternating current sources; Data collection; PC/104 modules.

Focuses on scientific materials and components. 3M Disposable IR Card; Four MegOhm insulation tester; Model 862 Dissolved Oxygen System with AUTO-STIR Self-stirring.

Presents scientific materials and components. Contraction actuators; Oil/water separators; Lenses.

Describes materials and components of scientific instruments. Fluid valves; Sample notchers; Packaging materials; High voltage supplies; Fiber optic filters; Membrane air dryers.

Features materials and components for scientific instruments. Local display module; Amplifier; Desuperheater; Analytical extractor; Time-to-digital converter; Molder; Memory card; Brakes; Solvent delivery; Manifold; Lithium battery; Vacuum transducer and switch; Infrared mounts; Sample changer; Photomultiplier tube; Flow indicators; Solar blind detector; Literature and software.

Features a selection of materials and components for scientific instruments and apparatus. Air compressor/vacuum pump; Triac scrubber; Electrophoresis columns; Spiking power supply; Laser diode controls; Multiplexer card; Data acquisition; Chromatography columns.

Features materials and components of various scientific instruments. Inclusion of Polytec PI Inc.'s piezoelectric translators that are ceramic actuators with subnanometer resolution and submillisecond response time; Daytronic Corp.'s SPS6000 Signal Processing System; Charlers Supper Co. Inc.'s nitrogen gas flow cooler; Henry G. Dietz Co. Inc.'s Model 192PDI pressurization monitor for cleanroom use.

In article number 1601168, Ho Shin Kim, Yaroslava G. Yingling, and co‐workers investigate the effect of graphene oxidation on the adsorption of poly‐thymine single‐stranded DNA (ssDNA) via all‐atom molecular dynamics simulations. The cover illustrates the conformational changes of folded ssDNA on graphene and graphene oxide surfaces. This study found that oxidation rate of graphene surface is correlated to the ssDNA structural stability. [ABSTRACT FROM AUTHOR]