Super-Suppression of Long-Wavelength Phonons in Constricted Nanoporous Geometries.

In a typical semiconductor material, the majority of the heat is carried by long-wavelength, long-mean-free-path phonons. Nanostructuring strategies to reduce thermal conductivity, a promising direction in the field of thermoelectrics, place scattering centers of size and spatial separation comparable to the mean free paths of the dominant phonons to selectively scatter them. The resultant thermal conductivity is in most cases well predicted using Matthiessen's rule. In general, however, long-wavelength phonons are not as effectively scattered as the rest of the phonon spectrum. In this work, using large-scale molecular-dynamics simulations, non-equilibrium Green's function simulations, and Monte Carlo simulations, we show that specific nanoporous geometries that create narrow constrictions in the passage of phonons lead to anticorrelated heat currents in the phonon spectrum. This effect results in super-suppression of long-wavelength phonons due to heat trapping and reductions in the thermal conductivity to values well below those predicted by Matthiessen's rule.

The Influence of Ions on the Electrochemical Stability of Aqueous Electrolytes.

The electrochemical stability window of water is known to vary with the type and concentration of dissolved salts. However, the underlying influence of ions on the thermodynamic stability of aqueous solutions has not been fully understood. Here, we investigated the electrolytic behaviors of aqueous electrolytes as a function of different ions. Our findings indicate that ions with high ionic potentials, i.e., charge density, promote the formation of their respective hydration structures, enhancing electrolytic reactions via an inductive effect, particularly for small cations. Conversely, ions with lower ionic potentials increase the proportion of free water molecules-those not engaged in hydration shells or hydrogen-bonding networks-leading to greater electrolytic stability. Furthermore, we observe that the chemical environment created by bulky ions with lower ionic potentials impedes electrolytic reactions by frustrating the solvation of protons and hydroxide ions, the products of oxygen evolution reaction (OER) and hydrogen evolution reaction (HER), respectively. We found that the solvation of protons plays a more substantial role than that of hydroxide, which explains a greater shift for OER than for HER, a puzzle that cannot be rationalized by the notion of varying O-H bond strengths of water. These insights will help the design of aqueous systems.

Metal-Mediated Directional Capping of Rod-Packing Metal-Organic Frameworks.

Two new rod-packing metal-organic frameworks (RPMOF) are constructed by regulating the in situ formation of the capping agent. In CPM-s7, carboxylate linkers extend 1D manganese-oxide chains in four additional directions, forming 3D RPMOF. The substitution of Mn2+ with a stronger Lewis acidic Co2+ , leads to an acceleration of the hydrolysis-prone sulfonate linker, resulting in presence of sulfate ions to reduce two out of the four carboxylate-extending directions, and thus forming a new 2D rod-packing CPM-s8. Density functional theory calculations and magnetization measurements reveal ferrimagnetic ordering of CPM-s8, signifying the potential of exploring 2D RPMOF for effective low-dimensional magnetic materials.

Enhanced Thermoelectric Performance of Polycrystalline Si0.8Ge0.2 Alloys through the Addition of Nanoscale Porosity.

Engineering materials to include nanoscale porosity or other nanoscale structures has become a well-established strategy for enhancing the thermoelectric performance of dielectrics. However, the approach is only considered beneficial for materials where the intrinsic phonon mean-free path is much longer than that of the charge carriers. As such, the approach would not be expected to provide significant performance gains in polycrystalline semiconducting alloys, such as SixGe1-x, where mass disorder and grains provide strong phonon scattering. In this manuscript, we demonstrate that the addition of nanoscale porosity to even ultrafine-grained Si0.8Ge0.2 may be worthwhile. The semiclassical Boltzmann transport equation was used to model electrical and phonon transport in polycrystalline Si0.8Ge0.2 containing prismatic pores perpendicular to the transport current. The models are free of tuning parameters and were validated against experimental data. The models reveal that a combination of pores and grain boundaries suppresses phonon conductivity to a magnitude comparable with the electronic thermal conductivity. In this regime, ZT can be further enhanced by reducing carrier concentration to the electrical and electronic thermal conductivity and simultaneously increasing thermopower. Although increases in ZT are modest, the optimal carrier concentration is significantly lowered, meaning semiconductors need not be so strongly supersaturated with dopants.

Reversible intercalation of methyl viologen as a dicationic charge carrier in aqueous batteries.

The interactions between charge carriers and electrode structures represent one of the most important considerations in the search for new energy storage devices. Currently, ionic bonding dominates the battery chemistry. Here we report the reversible insertion of a large molecular dication, methyl viologen, into the crystal structure of an aromatic solid electrode, 3,4,9,10-perylenetetracarboxylic dianhydride. This is the largest insertion charge carrier when non-solvated ever reported for batteries; surprisingly, the kinetic properties of the (de)insertion of methyl viologen are excellent with 60% of capacity retained when the current rate is increased from 100 mA g-1 to 2000 mA g-1. Characterization reveals that the insertion of methyl viologen causes phase transformation of the organic host, and embodies guest-host chemical bonding. First-principles density functional theory calculations suggest strong guest-host interaction beyond the pure ionic bonding, where a large extent of covalency may exist. This study extends the boundary of battery chemistry to large molecular ions as charge carriers and also highlights the electrochemical assembly of a supramolecular system.

Mg-Ion Battery Electrode: An Organic Solid's Herringbone Structure Squeezed upon Mg-Ion Insertion.

We report that crystalline 3,4,9,10-perylenetetracarboxylic dianhydride (PTCDA), an organic solid, is highly amenable to host divalent metal ions, i.e., Mg2+ and Ca2+, in aqueous electrolytes, where the van der Waals structure is intrinsically superior in hosting charge-dense ions. We observe that the divalent nature of Mg2+ causes unique squeezing deformation of the electrode structure, where it contracts and expands in different crystallographic directions when hosting the inserted Mg-ions. This phenomenon is revealed experimentally by ex situ X-ray diffraction and transmission electron microscopy, and is investigated theoretically by first-principles calculations. Interestingly, hosting one Mg2+ ion requires the coordination from three PTCDA molecules in adjacent columns of stacked molecules, which rotates the columns, thus reducing the (011) spacing but increasing the (021) spacing. We demonstrate that a PTCDA Mg-ion electrode delivers a reversible capacity of 125 mA h g-1, which may include a minor contribution of hydronium storage, a good rate capability by retaining 75 mA h g-1 at 500 mA g-1 (or 3.7 C), and a stable cycle life. We also report Ca2+ storage in PTCDA, where a reversible capacity of over 80 mA h g-1 is delivered.

Method to manage integration error in the Green-Kubo method.

The Green-Kubo method is a commonly used approach for predicting transport properties in a system from equilibrium molecular dynamics simulations. The approach is founded on the fluctuation dissipation theorem and relates the property of interest to the lifetime of fluctuations in its thermodynamic driving potential. For heat transport, the lattice thermal conductivity is related to the integral of the autocorrelation of the instantaneous heat flux. A principal source of error in these calculations is that the autocorrelation function requires a long averaging time to reduce remnant noise. Integrating the noise in the tail of the autocorrelation function becomes conflated with physically important slow relaxation processes. In this paper we present a method to quantify the uncertainty on transport properties computed using the Green-Kubo formulation based on recognizing that the integrated noise is a random walk, with a growing envelope of uncertainty. By characterizing the noise we can choose integration conditions to best trade off systematic truncation error with unbiased integration noise, to minimize uncertainty for a given allocation of computational resources.

Hydronium-Ion Batteries with Perylenetetracarboxylic Dianhydride Crystals as an Electrode.

We demonstrate for the first time that hydronium ions can be reversibly stored in an electrode of crystalline 3,4,9,10-perylenetetracarboxylic dianhydride (PTCDA). PTCDA exhibits a capacity of 85 mAh g-1 at 1 A g-1 after an initial conditioning process. Ex situ X-ray diffraction revealed reversible and significant structure dilation upon reduction of PTCDA in an acidic electrolyte, which can only be ascribed to hydronium-ion intercalation. The lattice expansion upon hydronium storage was theoretically explored by first-principles density functional theory (DFT) calculations, which confirmed the hydronium storage in PTCDA.

Automated design of flexible linkers.

This paper presents a method for the systematic and automated design of flexible organic linkers for construction of metal organic-frameworks (MOFs) in which flexibility, compliance, or other mechanically exotic properties originate at the linker level rather than from the framework kinematics. Our method couples a graph grammar method for systematically generating linker like molecules with molecular dynamics modeling of linkers' mechanical response. Using this approach we have generated a candidate pool of >59,000 hypothetical linkers. We screen linker candidates according to their mechanical behaviors under large deformation, and extract fragments common to the most performant candidate materials. To demonstrate the general approach to MOF design we apply our system to designing linkers for pressure switching MOFs-MOFs that undergo reversible structural collapse after a stress threshold is exceeded.

Phonostat: thermostatting phonons in molecular dynamics simulations.

Thermostat algorithms in a molecular dynamics simulation maintain an average temperature of a system by regulating the atomic velocities rather than the internal degrees of freedom. Herein, we present a "phonostat" algorithm that can regulate the total energy in a given internal degree of freedom. In this algorithm, the modal energies are computed at each time step using a mode-tracking scheme and then the system is driven by an external driving force of desired frequency and amplitude. The rate and amount of energy exchange between the phonostat and the system is controlled by two distinct damping parameters. Two different schemes for controlling the external driving force amplitude are also presented. In order to test our algorithm, the method is applied initially to a simple anharmonic oscillator for which the role of various phonostat parameters can be carefully tested. We then apply the phonostat to a more realistic (10,0) carbon nanotube system and show how such an approach can be used to regulate energy of highly anharmonic modes.

A novel potent Fas agonist for selective depletion of tumor cells in hematopoietic transplants.

There remains a clear need for effective tumor cell purging in autologous stem cell transplantation (ASCT) where residual malignant cells within the autograft contribute to disease relapse. Here we propose the use of a novel Fas agonist with potent pro-apoptotic activity, termed MegaFasL, as an effective ex-vivo purging agent. MegaFasL selectively kills hematological cancer cells from lymphomas and leukemias and prevents tumor development at concentrations that do not reduce the functional capacity of human hematopoietic stem/progenitor cells both in in vitro and in in vivo transplantation models. These findings highlight the potential use of MegaFasL as an ex-vivo purging agent in ASCT.

Anomalous dissipation in single-walled carbon nanotube resonators.

We observe a new anomalous and transient process of intrinsic dissipation in simulations of the ring-down of flexural modes in single-walled carbon nanotube (CNT) resonators. The effect is pronounced, causing the quality factor of the mode to be reduced by more that 95% for tens of picoseconds. The anomalous dissipation depends on the CNT temperature and the energy in the mode, and remarkably increasing the excitation energy in the resonator causes it to decay to zero faster. By tracking the cascade of energy as it dissipates we identify "gateway" modes that provide important channels for dissipation. The processes we observe show that an athermal phonon population accompanying dissipation can strongly influence the quality factor in nanoelectromechanical devices.

Nanomechanical resonance spectroscopy: a novel route to ultrasensitive label-free detection.

We propose a new chemical detection technique in which an analyte's vibrational frequencies are interrogated directly using an array of nanomechanical resonators. This "nanomechanical resonance spectroscopy" (NRS) could permit label-free chemical detection, combining the high sensitivity of nanomechanical approaches with the high selectivity of traditional spectroscopy. A computational proof of principle is presented, demonstrating the central concept: exploiting resonant exchange of vibrational energy for chemical identification. Guidelines for experimental realization of NRS are discussed.

Nanomechanical energy transfer and resonance effects in single-walled carbon nanotubes.

Molecular dynamics simulations are employed to elucidate the important factors in mechanical energy transfer between carbon nanotubes. Our calculations show that sharp resonance effects allow for near complete and highly efficient energy transfer. In addition, the weak coupling between two nanotubes sets the time scale for the energy transfer. The simulations provide the mechanistic basis for a theoretical description of lattice vibration mediated heat flow in nanoscale materials.

Metal-induced assembly of a semiconductor island lattice: Ge truncated pyramids on Au-patterned Si.

We report the two-dimensional alignment of semiconductor islands using rudimentary metal patterning to control nucleation and growth. In the Ge on Si system, a square array of submicron Au dots on the Si (001) surface induces the assembly of deposited Ge adatoms into an extensive island lattice. Remarkably, these highly ordered Ge islands form between the patterned Au dots and are characterized by a unique truncated pyramidal shape. A model based on patterned diffusion barriers explains the observed ordering and establishes general criteria for the broader applicability of such a directed assembly process to quantum dot ordering.

Drug-like annotation and duplicate analysis of a 23-supplier chemical database totalling 2.7 million compounds.

We have implemented five drug-like filters, based on 1D and 2D molecular descriptors, and applied them to characterize the drug-like properties of commercially available chemical compounds. In addition to previously published filters (Lipinski and Veber), we implemented a filter for medicinal chemistry tractability based on lists of chemical features drawn up by a panel of medicinal chemists. A filter based on the modeling of aqueous solubility (>1 microM) was derived in-house, as well as another based on the modeling of Caco-2 passive membrane permeability (>10 nm/s). A library of 2.7 million compounds was collated from the 23 compound suppliers and analyzed with these filters, highlighting a tendency toward highly lipophilic compounds. The library contains 1.6 M unique structures, of which 37% (607,223) passed all five drug-like filters. None of the 23 suppliers provides all the members of the drug-like subset, emphasizing the benefit of considering compounds from various compound suppliers as a source of diversity for drug discovery.

Adatom transport on strained Cu(001): surface crowdions.

Surface strain is often suggested as a means to control the self-assembled growth of nanostructures. Strain affects both the kinetics of nucleation and the free energies of formation of the desired nanostructure. It is demonstrated here that diffusion on some strained surfaces may be mediated by newly identified adatom transport mechanism: the formation and motion of a surface crowdion.

Serum response factor cleavage by caspases 3 and 7 linked to apoptosis in human BJAB cells.

Apoptosis involves the cessation of cellular processes, the breakdown of intracellular organelles, and, finally, the nonphlogistic clearance of apoptotic cells from the body. Important for these events is a family of proteases, caspases, which are activated by a proteolytic cleavage cascade and drive apoptosis by targeting key proteins within the cell. Here, we demonstrate that serum response factor (SRF), a transcription factor essential for proliferative gene expression, is cleaved by caspases and that this cleavage occurs in proliferating murine fibroblasts and can be induced in the human B-cell line BJAB. We identify the two major sites at which SRF cleavage occurs as Asp(245) and Asp(254), the caspases responsible for the cleavage and generate a mutant of SRF resistant to cleavage in BJAB cells. Investigation of the physiological and functional significance of SRF cleavage reveals that it correlates with the loss of c-fos expression, whereby neither SRF cleavage fragment retains transcriptional activity. Moreover, the expression of a noncleavable SRF in BJAB cells suppresses apoptosis induced by Fas cross-linking. These results suggest that for apoptosis to proceed, the transcriptional events promoting cell survival and proliferation, in which SRF is involved, must first be inactivated.

Statistical comparison of established T-cell epitope predictors against a large database of human and murine antigens.

Identification of T-cell epitopes within a protein antigen is an important tool in vaccine design. The T-cell epitope prediction schemes often are exploited by workers but have proved unreliable in comparison with experimental techniques. We compared published T-cell epitope predictors against two databases of human and murine T-cell epitopes. Each predictor was assessed against random cyclic permutations of epitopes in order to determine significance. Predictor performance was expressed in terms of two parameters, specificity and sensitivity. Specificity is an expression of the quality of predictions, whereas sensitivity is an expression of the quantity of epitopes predicted. Against the human data set, the strip-of-hydrophobic helix algorithm [Stille et al., Molec. Immun. 24, 1021-1027 (1987)] was the only significant predictor (p < 0.05), whereas against murine data only, the Roth2 pattern [Rothbard and Taylor, EMBO J. 7, 93-100 (1988)] was significant (p < 0.05). Not only were the majority of algorithms no better than random against both data sets, against the murine data two schemes were significant (p < 0.05) anti-predictors. This report indicates which predictors are relevant statistically and is the first to describe anti-predictors which can themselves be useful in the identification of T-cell epitopes.