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Understanding the thermal transport mechanisms in amorphous organic materials is of great importance to solve hot-spot issues in organic-electronics nanodevices. Here we studied thermal transport in two popular molecular electronic materials, N,N-dicarbazolyl-3,5-benzene (mCP) and N,N'-diphenyl-N,N'-di(3-methylphenyl)-(1,1'-biphenyl)-4,4'diamine (TPD), in the amorphous state by molecular dynamics simulations. We found that due to the softness of organic materials, the low thermal conductivity of both systems can be greatly enhanced under pressure. Notably, in such systems, the convective term of heat flux provides an important contribution to thermal transport as it cross-correlates with the Virial term in the Green-Kubo formula. Mode diffusivity calculations reveal that low-frequency modes can contribute significantly to thermal transport in both mCP and TPD. By increasing the pressure, the sound velocity and relaxation time of such low-frequency modes can be enhanced, and a part of these modes converts from diffusons to propagons. The cooperation of these three effects is responsible for the strong pressure dependence of thermal transport in amorphous organic systems. Molecular pair heat flux calculations demonstrate that heat transfer mainly happens between pairs of molecules with distances below 1.4 nm. This work paves the way for the optimization of thermal transport in amorphous organic materials widely used in opto-electronics, e.g. as OLED and OPV.

Three novel unconventional clathrates with unprecedented III-V semiconducting frameworks have been synthesized: Cs 8 In 27 Sb 19 , Cs 8 Ga 27 Sb 19 , and Rb 8 Ga 27 Sb 19 . These clathrates represent the first examples of tetrel-free clathrates that are completely composed of main group elements. All title compounds crystallize in an ordered superstructure of clathrate-I in the Ia 3̅ space group (No. 206; Z = 8). In the clathrate framework, a full ordering of {Ga or In} and Sb is observed by a combination of high-resolution synchrotron single-crystal and powder X-ray diffraction techniques. Density functional theory (DFT) calculations show that all three clathrates are energetically stable with relaxed lattice constants matching the experimental data. Due to the complexity of the crystal structure composed of heavy elements, the reported clathrates exhibit ultralow thermal conductivities of less than 1 W·m -1 ·K -1 at room temperature. All compounds are predicted and experimentally confirmed to be narrow-bandgap p-type semiconductors with high Seebeck thermopower values, up to 250 μV·K -1 at 300 K for Cs 8 In 27 Sb 19 . The latter compound shows carrier concentrations and mobilities, 1.42 × 10 15 cm -3 and 880 cm 2 ·V -1 ·s -1 , which are on par with the values for parent binary InSb, one of the best electronic semiconductors. The high hole carrier mobility is uncommon for complex bulk materials and a highly desirable trait, opening ways to design semiconducting materials based on tunable III-V clathrates.

Nonequilibrium molecular dynamics (NEMD) has been extensively used to study thermal transport at various length scales in many materials. In this method, two local thermostats at different temperatures are used to generate a nonequilibrium steady state with a constant heat flux. Conventionally, the thermal conductivity of a finite system is calculated as the ratio between the heat flux and the temperature gradient extracted from the linear part of the temperature profile away from the local thermostats. Here, we show that, with a proper choice of the thermostat, the nonlinear part of the temperature profile should actually not be excluded in thermal transport calculations. We compare NEMD results against those from the atomistic Green's function method in the ballistic regime and those from the homogeneous nonequilibrium molecular dynamics method in the ballistic-to-diffusive regime. These comparisons suggest that in all the transport regimes, one should directly calculate the thermal conductance from the temperature difference between the heat source and sink and, if needed, convert it into the thermal conductivity by multiplying it with the system length. Furthermore, we find that the Langevin thermostat outperforms the Nosé-Hoover (chain) thermostat in NEMD simulations because of its stochastic and local nature. We show that this is particularly important for studying asymmetric carbon-based nanostructures, for which the Nosé-Hoover thermostat can produce artifacts leading to unphysical thermal rectification.

We introduce a novel approach to model heat transport in solids, based on the Green-Kubo theory of linear response. It naturally bridges the Boltzmann kinetic approach in crystals and the Allen-Feldman model in glasses, leveraging interatomic force constants and normal-mode linewidths computed at mechanical equilibrium. At variance with molecular dynamics, our approach naturally and easily accounts for quantum mechanical effects in energy transport. Our methodology is carefully validated against results for crystalline and amorphous silicon from equilibrium molecular dynamics and, in the former case, from the Boltzmann transport equation.

Infrared pump-probe spectroscopy provides detailed information about the dynamics of hydrogen-bonded liquids. Due to dissipation of the absorbed pump pulse energy, thermal equilibration dynamics also contributes to the observed signal. Disentangling this contribution from the molecular response remains a challenge. By performing non-equilibrium molecular dynamics simulations of liquid-deuterated methanol, we show that faster molecular vibrational relaxation and slower heat diffusion are decoupled and occur on different length scales. Transient structures of the hydrogen bonding network influence thermal relaxation by affecting thermal diffusivity over a length scale of several nanometers.

Layered two-dimensional (2D) materials have highly anisotropic thermal properties between the in-plane and cross-plane directions. Conventionally, it is thought that cross-plane thermal conductivities (κ z ) are low, and therefore c-axis phonon mean free paths (MFPs) are small. Here, we measure κ z across MoS 2 films of varying thickness (20-240 nm) and uncover evidence of very long c-axis phonon MFPs at room temperature in these layered semiconductors. Experimental data obtained using time-domain thermoreflectance (TDTR) are in good agreement with first-principles density functional theory (DFT). These calculations suggest that ∼50% of the heat is carried by phonons with MFP > 200 nm, exceeding kinetic theory estimates by nearly 2 orders of magnitude. Because of quasi-ballistic effects, the κ z of nanometer-thin films of MoS 2 scales with their thickness and the volumetric thermal resistance asymptotes to a nonzero value, ∼10 m 2 K GW -1 . This contributes as much as 30% to the total thermal resistance of a 20 nm thick film, the rest being limited by thermal interface resistance with the SiO 2 substrate and top-side aluminum transducer. These findings are essential for understanding heat flow across nanometer-thin films of MoS 2 for optoelectronic and thermoelectric applications.

Importance: Professional use of pesticides is a risk factor for non-Hodgkin lymphoma. The main biological mechanisms of pesticides and chemotherapy are genotoxicity and reactive oxygen species generation. Cellular adaptation among patients exposed to low doses of genotoxic and oxidative compounds might hinder chemotherapy efficiency in patients with lymphoma., Objective: To examine the association of occupational exposure to pesticides with immunochemotherapy response and survival among patients treated for diffuse large B-cell lymphoma., Design, Setting, and Participants: This retrospective cohort study assessed patients treated from July 1, 2010, to May 31, 2015, for diffuse large B-cell lymphoma, with a 2-year follow-up. The study took place at 6 university and nonuniversity hospitals in Languedoc-Roussillon, France. A total of 404 patients with newly diagnosed diffuse large B-cell lymphoma treated with anthracycline-based immunochemotherapy were included before the study began. Occupational history was reconstructed for 244 patients and analyzed with the PESTIPOP French job-exposure matrix to determine likelihood of occupational exposure to pesticides. Analysis of the data was performed from July 15, 2017, to July 15, 2018., Main Outcomes and Measures: Treatment failure (ie, partial response, stable disease, disease progression, or interruption for toxic effects) rate, 2-year event-free survival, and overall survival between exposed and nonexposed patients after adjustment for confounding factors., Results: A total of 244 patients (mean [SD] age, 61.3 [15.2] years; 153 [62.7%] male) had complete occupational data. Of these patients, 67 (27.4%) had occupational exposure to pesticides, with 38 exposed through agricultural occupations. Occupational exposure was not associated with clinical and biological characteristics at diagnosis. Occupationally exposed patients had a significantly higher treatment failure rate (22.4% vs 11.3%; P = .03; adjusted odds ratio [AOR] for confounding factors, 3.0; 95% CI, 1.3-6.9); this difference was higher among patients with exposing agricultural occupations compared with other patients (29.0% vs 11.7%; AOR, 5.1; 95% CI, 2.0-12.8). Two-year event-free survival was 70% in the occupationally exposed group vs 82% in the unexposed group (adjusted hazard ratio [AHR] for confounding factors, 2.2; 95% CI, 1.3-3.9). Among patients with exposing agricultural occupations compared with other patients, the difference was more pronounced (2-year event-free survival, 56% vs 83%; AHR, 3.5; 95% CI, 1.9-6.5). Similarly, 2-year overall survival was lower in the group of patients with exposing agricultural occupations compared with other patients (81% vs 92%; AHR, 3.9; 95% CI, 1.5-10.0)., Conclusions and Relevance: This retrospective study showed that agricultural occupational exposure to pesticides was associated with treatment failure, event-free survival, and overall survival among patients with diffuse large B-cell lymphoma.

The ability to actively regulate heat flow at the nanoscale could be a game changer for applications in thermal management and energy harvesting. Such a breakthrough could also enable the control of heat flow using thermal circuits, in a manner analogous to electronic circuits. Here we demonstrate switchable thermal transistors with an order of magnitude thermal on/off ratio, based on reversible electrochemical lithium intercalation in MoS 2 thin films. We use spatially-resolved time-domain thermoreflectance to map the lithium ion distribution during device operation, and atomic force microscopy to show that the lithiated state correlates with increased thickness and surface roughness. First principles calculations reveal that the thermal conductance modulation is due to phonon scattering by lithium rattler modes, c-axis strain, and stacking disorder. This study lays the foundation for electrochemically-driven nanoscale thermal regulators, and establishes thermal metrology as a useful probe of spatio-temporal intercalant dynamics in nanomaterials.

Water molecules adsorbed on inorganic substrates play an important role in several technological applications. In the presence of light atoms in adsorbates, nuclear quantum effects (NQEs) influence the structural stability and the dynamical properties of these systems. In this work, we explore the impact of NQEs on the dissociation of water wires on stepped Pt(221) surfaces. By performing ab initio molecular dynamics simulations with van der Waals corrected density functional theory, we note that several competing minima for both intact and dissociated structures are accessible at finite temperatures, making it important to assess whether harmonic estimates of the quantum free energy are sufficient to determine the relative stability of the different states. We thus perform ab initio path integral molecular dynamics (PIMD) in order to calculate these contributions taking into account the conformational entropy and anharmonicities at finite temperatures. We propose that when adsorption is weak and NQEs on the substrate are negligible, PIMD simulations can be performed through a simple partition of the system, resulting in considerable computational savings. We then calculate the full contribution of NQEs to the free energies, including also anharmonic terms. We find that they result in an increase of up to 20% of the quantum contribution to the dissociation free energy compared with the harmonic estimates. We also find that the dissociation process has a negligible contribution from tunneling but is dominated by zero point energies, which can enhance the rate of dissociation by three orders of magnitude. Finally we highlight how both temperature and NQEs indirectly impact dipoles and the redistribution of electron density, causing work function changes of up to 0.4 eV with respect to static estimates. This quantitative determination of the change in the work function provides a possible approach to determine experimentally the most stable configurations of water oligomers on the stepped surfaces.

Thermal rectification is of importance not only for fundamental physics, but also for potential applications in thermal manipulations and thermal management. However, thermal rectification effect usually decays rapidly with system size. Here, we show that a mass-graded system, with two diffusive leads separated by a ballistic spacer, can exhibit large thermal rectification effect, with the rectification factor independent of system size. The underlying mechanism is explained in terms of the effective size-independent thermal gradient and the match or mismatch of the phonon bands. We also show the robustness of the thermal diode upon variation of the model's parameters. Our finding suggests a promising way for designing realistic efficient thermal diodes.

Grain boundaries in graphene are inherent in wafer-scale samples prepared by chemical vapor deposition. They can strongly influence the mechanical properties and electronic and heat transport in graphene. In this work, we employ extensive molecular dynamics simulations to study thermal transport in large suspended polycrystalline graphene samples. Samples of different controlled grain sizes are prepared by a recently developed efficient multiscale approach based on the phase field crystal model. In contrast to previous works, our results show that the scaling of the thermal conductivity with the grain size implies bimodal behavior with two effective Kapitza lengths. The scaling is dominated by the out-of-plane (flexural) phonons with a Kapitza length that is an order of magnitude larger than that of the in-plane phonons. We also show that, to get quantitative agreement with the most recent experiments, quantum corrections need to be applied to both the Kapitza conductance of grain boundaries and the thermal conductivity of pristine graphene, and the corresponding Kapitza lengths must be renormalized accordingly.

We introduce a nonequilibrium molecular dynamics simulation approach, based on the generalized Langevin equation, to study vibrational energy relaxation in pump-probe spectroscopy. A colored noise thermostat is used to selectively excite a set of vibrational modes, leaving the other modes nearly unperturbed, to mimic the effect of a monochromatic laser pump. Energy relaxation is probed by analyzing the evolution of the system after excitation in the microcanonical ensemble, thus providing direct information about the energy redistribution paths at the molecular level and their time scale. The method is applied to hydrogen-bonded molecular liquids, specifically deuterated methanol and water, providing a robust picture of energy relaxation at the molecular scale.

On the surface of water ice, a quasi-liquid layer (QLL) has been extensively reported at temperatures below its bulk melting point at 273 K. Approaching the bulk melting temperature from below, the thickness of the QLL is known to increase. To elucidate the precise temperature variation of the QLL, and its nature, we investigate the surface melting of hexagonal ice by combining noncontact, surface-specific vibrational sum frequency generation (SFG) spectroscopy and spectra calculated from molecular dynamics simulations. Using SFG, we probe the outermost water layers of distinct single crystalline ice faces at different temperatures. For the basal face, a stepwise, sudden weakening of the hydrogen-bonded structure of the outermost water layers occurs at 257 K. The spectral calculations from the molecular dynamics simulations reproduce the experimental findings; this allows us to interpret our experimental findings in terms of a stepwise change from one to two molten bilayers at the transition temperature., Competing Interests: The authors declare no conflict of interest.

The adsorption of phenol and phenoxy on the (111) surface of Au and Pt has been investigated by density functional theory calculations with the conventional PBE functional and three different non-local van der Waals (vdW) exchange and correlation functionals. It is found that both phenol and phenoxy on Au(111) are physisorbed. In contrast, phenol on Pt(111) presents an adsorption energy profile with a stable chemisorption state and a weakly metastable physisorbed precursor. While the use of vdW functionals is essential to determine the correct binding energy of both chemisorption and physisorption states, the relative stability and existence of an energy barrier between them depend on the semi-local approximations in the functionals. The first dissociation mechanism of phenol, yielding phenoxy and atomic hydrogen, has been also investigated, and the reaction and activation energies of the resulting phenoxy on the flat surfaces of Au and Pt were discussed.

Adaptive quantum mechanical (QM)/molecular mechanical (MM) methods enable efficient molecular simulations of chemistry in solution. Reactive subregions are modeled with an accurate QM potential energy expression while the rest of the system is described in a more approximate manner (MM). As solvent molecules diffuse in and out of the reactive region, they are gradually included into (and excluded from) the QM expression. It would be desirable to model such a system with a single adaptive Hamiltonian, but thus far this has resulted in distorted structures at the boundary between the two regions. Solving this long outstanding problem will allow microcanonical adaptive QM/MM simulations that can be used to obtain vibrational spectra and dynamical properties. The difficulty lies in the complex QM potential energy expression, with a many-body expansion that contains higher order terms. Here, we outline a Hamiltonian adaptive multiscale scheme within the framework of many-body potentials. The adaptive expressions are entirely general, and complementary to all standard (nonadaptive) QM/MM embedding schemes available. We demonstrate the merit of our approach on a molecular system defined by two different MM potentials (MM/MM'). For the long-range interactions a numerical scheme is used (particle mesh Ewald), which yields energy expressions that are many-body in nature. Our Hamiltonian approach is the first to provide both energy conservation and the correct solvent structure everywhere in this system.

Quantum delocalization of atomic nuclei affects the physical properties of many hydrogen-rich liquids and biological systems even at room temperature. In computer simulations, quantum nuclei can be modeled via the path-integral formulation of quantum statistical mechanics, which implies a substantial increase in computational overhead. By restricting the quantum description to a small spatial region, this cost can be significantly reduced. Herein, we derive a bottom-up, rigorous, Hamiltonian-based scheme that allows molecules to change from quantum to classical and vice versa on the fly as they diffuse through the system, both reducing overhead and making quantum grand-canonical simulations possible. The method is validated via simulations of low-temperature parahydrogen. Our adaptive resolution approach paves the way to efficient quantum simulations of biomolecules, membranes, and interfaces.

Understanding the design rules to obtain materials that enable a tight control of phonon transport over a broad range of frequencies would aid major developments in thermoelectric energy harvesting, heat management in microelectronics, and information and communication technology. Using atomistic simulations we show that the metamaterials approach relying on localized resonances is very promising to engineer heat transport at the nanoscale. Combining designed resonant structures to alloying can lead to extremely low thermal conductivity in silicon nanowires. The hybridization between resonant phonons and propagating modes greatly reduces the group velocities and the phonon mean free paths in the low frequency acoustic range below 4 THz. Concurrently, alloy scattering hinders the propagation of high frequency thermal phonons. Our calculations establish a rationale between the size, shape, and period of the resonant structures, and the thermal conductivity of the nanowire, and demonstrate that this approach is even effective to block phonon transport in wavelengths much longer than the size and period of the surface resonant structures. A further consequence of using resonant structures is that they are not expected to scatter electrons, which is beneficial for thermoelectric applications.

Most ice in nature forms because of impurities which boost the exceedingly low nucleation rate of pure supercooled water. However, the microscopic details of ice nucleation on these substances remain largely unknown. Here, we have unraveled the molecular mechanism and the kinetics of ice formation on kaolinite, a clay mineral playing a key role in climate science. We find that the formation of ice at strong supercooling in the presence of this clay is about 20 orders of magnitude faster than homogeneous freezing. The critical nucleus is substantially smaller than that found for homogeneous nucleation and, in contrast to the predictions of classical nucleation theory (CNT), it has a strong two-dimensional character. Nonetheless, we show that CNT describes correctly the formation of ice at this complex interface. Kaolinite also promotes the exclusive nucleation of hexagonal ice, as opposed to homogeneous freezing where a mixture of cubic and hexagonal polytypes is observed.

Thermoelectric materials are strategically valuable for sustainable development, as they allow for the generation of electrical energy from wasted heat. In recent years several strategies have demonstrated some efficiency in improving thermoelectric properties. Dopants affect carrier concentration, while thermal conductivity can be influenced by alloying and nanostructuring. Features at the nanoscale positively contribute to scattering phonons, however those with long mean free paths remain difficult to alter. Here we use the concept of hierarchical nano-grains to demonstrate thermal conductivity reduction in rocksalt lead chalcogenides. We demonstrate that grains can be obtained by taking advantage of the reconstructions along the phase transition path that connects the rocksalt structure to its high-pressure form. Since grain features naturally change as a function of size, they impact thermal conductivity over different length scales. To understand this effect we use a combination of advanced molecular dynamics techniques to engineer grains and to evaluate thermal conductivity in PbSe. By affecting grain morphologies only, i.e. at constant chemistry, two distinct effects emerge: the lattice thermal conductivity is significantly lowered with respect to the perfect crystal, and its temperature dependence is markedly suppressed. This is due to an increased scattering of low-frequency phonons by grain boundaries over different size scales. Along this line we propose a viable process to produce hierarchical thermoelectric materials by applying pressure via a mechanical load or a shockwave as a novel paradigm for material design.

A detailed understanding of the connections of fabrication and processing to structural and thermal properties of low-dimensional nanostructures is essential to design materials and devices for phononics, nanoscale thermal management, and thermoelectric applications. Silicon provides an ideal platform to study the relations between structure and heat transport since its thermal conductivity can be tuned over 2 orders of magnitude by nanostructuring. Combining realistic atomistic modeling and experiments, we unravel the origin of the thermal conductivity reduction in ultrathin suspended silicon membranes, down to a thickness of 4 nm. Heat transport is mostly controlled by surface scattering: rough layers of native oxide at surfaces limit the mean free path of thermal phonons below 100 nm. Removing the oxide layers by chemical processing allows us to tune the thermal conductivity over 1 order of magnitude. Our results guide materials design for future phononic applications, setting the length scale at which nanostructuring affects thermal phonons most effectively.

The Adaptive Resolution Scheme (AdResS) is a hybrid scheme that allows to treat a molecular system with different levels of resolution depending on the location of the molecules. The construction of a Hamiltonian based on the this idea (H-AdResS) allows one to formulate the usual tools of ensembles and statistical mechanics. We present a number of exact and approximate results that provide a statistical mechanics foundation for this simulation method. We also present simulation results that illustrate the theory.

The energy stored in the triplet states of organic molecules, capable of energy transfer via an emissive process (phosphorescence) or a nonemissive process (triplet-triplet transfer), is actively dissipated in the presence of molecular oxygen. The reason is that photoexcited singlet oxygen is highly reactive, so the photoactive molecules in the system are quickly oxidized. Oxidation leads to further loss of efficiency and various undesirable side effects. In this work we have developed a structurally diverse library of hyperbranched unsaturated poly(phosphoester)s that allow efficient scavenging of singlet oxygen, but do not react with molecular oxygen in the ground state, i.e., triplet state. The triplet-triplet annihilation photon upconversion was chosen as a highly oxygen-sensitive process as proof for a long-term protection against singlet oxygen quenching, with comparable efficiencies of the photon upconversion under ambient conditions as in an oxygen-free environment in several unsaturated polyphosphates. The experimental results are further correlated to NMR spectroscopy and theoretical calculations evidencing the importance of the phosphate center. These results open a technological window toward efficient solar cells but also for sustainable solar upconversion devices, harvesting a broad-band sunlight excitation spectrum.

Graphene exhibits extraordinary electronic and mechanical properties, and extremely high thermal conductivity. Being a very stable atomically thick membrane that can be suspended between two leads, graphene provides a perfect test platform for studying thermal conductivity in two-dimensional systems, which is of primary importance for phonon transport in low-dimensional materials. Here we report experimental measurements and non-equilibrium molecular dynamics simulations of thermal conduction in suspended single-layer graphene as a function of both temperature and sample length. Interestingly and in contrast to bulk materials, at 300 K, thermal conductivity keeps increasing and remains logarithmically divergent with sample length even for sample lengths much larger than the average phonon mean free path. This result is a consequence of the two-dimensional nature of phonons in graphene, and provides fundamental understanding of thermal transport in two-dimensional materials.

Many well-established classical biomolecular force fields, fitted on the solvation properties of single ions, do not necessarily describe all the details of ion pairing accurately, especially for complex polyatomic ions. Depending on the target application, it might not be sufficient to reproduce the thermodynamics of ion pairing, but it may also be necessary to correctly capture structural details, such as the coordination mode. In this work, we analyzed how classical force fields can be optimized to yield a realistic description of these different aspects of ion pairing. Given the prominent role of the interactions of negatively charged amino-acid side chains and divalent cations in many biomolecular systems, we chose calcium acetate as a benchmark system to devise a general optimization strategy that we applied to two popular force fields, namely, GROMOS and OPLS-AA. Using experimental association constants and first-principles molecular dynamics simulations as a reference, we found that small modifications of the van der Waals ion-ion interaction parameters allow a systematic improvement of the essential thermodynamic and structural properties of ion pairing.

We outline a method to investigate the role of nuclear quantum effects in liquid water making use of a force field derived from ab initio simulations. Starting from a first-principles molecular dynamics simulation, we obtain an effective force field for bulk liquid water using the force-matching technique. After validating that our effective model reproduces the key structural and dynamic properties of the reference system, we use it to perform path integral simulations to investigate the role played by nuclear quantum effects on bulk water, probing radial distribution functions, vibrational spectra, and hydrogen bond fluctuations. Our approach offers a practical route to derive ab initio quality molecular models to study quantum effects at a low computational cost.

The mechanism of particle formation from submicrometer emulsion droplets by solvent evaporation is revisited. A combination of dynamic light scattering, fluorescence resonance energy transfer, zeta potential measurements, and fluorescence cross-correlation spectroscopy is used to analyze the colloids during the evaporation process. It is shown that a combination of different methods yields reliable and quantitative data for describing the fate of the droplets during the process. The results indicate that coalescence plays a minor role during the process; the relatively large size distribution of the obtained polymer colloids can be explained by the droplet distribution after their formation., (Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.)

Complex soft matter systems can be efficiently studied with the help of adaptive resolution simulation methods, concurrently employing two levels of resolution in different regions of the simulation domain. The nonmatching properties of high- and low-resolution models, however, lead to thermodynamic imbalances between the system's subdomains. Such inhomogeneities can be healed by appropriate compensation forces, whose calculation requires nontrivial iterative procedures. In this work we employ the recently developed Hamiltonian adaptive resolution simulation method to perform Monte Carlo simulations of a binary mixture, and propose an efficient scheme, based on Kirkwood thermodynamic integration, to regulate the thermodynamic balance of multicomponent systems.

Adaptive resolution schemes allow the simulation of a molecular fluid treating simultaneously different subregions of the system at different levels of resolution. In this work we present a new scheme formulated in terms of a global Hamiltonian. Within this approach equilibrium states corresponding to well-defined statistical ensembles can be generated making use of all standard molecular dynamics or Monte Carlo methods. Models at different resolutions can thus be coupled, and thermodynamic equilibrium can be modulated keeping each region at desired pressure or density without disrupting the Hamiltonian framework.

At a given thermodynamic condition, nucleation events occur at a frequency that scales with the volume of the system. Therefore at the nanoscale, one may expect to obtain supercooled liquids below the bulk homogeneous nucleation temperature. Here we report direct computational evidence that in supercooled water nano-droplets ice nucleation rates are strongly size dependent and at the nanoscale they are several orders of magnitude smaller than in bulk water. Using a thermodynamic model based on classical nucleation theory, we show that the Laplace pressure is partially responsible for the suppression of ice crystallization. Our simulations show that the nucleation rates found for droplets are similar to those of liquid water subject to a pressure of the order of the Laplace pressure within droplets. Our findings aid the interpretation of molecular beam experiments and support the hypothesis of surface crystallization of ice in microscopic water droplets in clouds.

This paper presents a theoretical investigation of the microscopic mechanisms responsible for heat transport in bulk Si, Ge and SiGe alloys, with the goal of providing insight into design rules for efficient Si-based nanostructured thermoelectric semiconductors. We carried out a detailed atomistic study of the thermal conductivity, using molecular dynamics and the Boltzmann transport equation. We investigated in detail the effects of the physical approximations underlying each approach, as well as the effect of the numerical approximations involved in the implementation of the two different methods. Our findings permitted us to understand and reconcile apparently conflicting results reported in the literature.

Water-metal interfaces are ubiquitous and play a key role in many chemical processes, from catalysis to corrosion. Whereas water adlayers on atomically flat transition metal surfaces have been investigated in depth, little is known about the chemistry of water on stepped surfaces, commonly occurring in realistic situations. Using first-principles simulations, we study the adsorption of water on a stepped platinum surface. We find that water adsorbs preferentially at the step edge, forming linear clusters or chains, stabilized by the cooperative effect of chemical bonds with the substrate and hydrogen bonds. In contrast with their behavior on flat Pt, at steps water molecules dissociate, forming mixed hydroxyl/water structures, through an autocatalytic mechanism promoted by H-bonding. Nuclear quantum effects contribute to stabilize partially dissociated cluster and chains. Together with the recently demonstrated behavior of water chains adsorbed on stepped Pt surfaces to transfer protons via thermally activated hopping, these findings make these systems viable candidates for proton wires.

Bottom-up fabrication of graphene nanoribbons (GNRs) from halogen-terminated aromatic precursors is a promising method for achieving atomically precise nanoribbons at competitive yields. GNR fabrication proceeds via the polymerization of the precursors and successive dehydrogenation. By first principles density functional theory calculations, we perform a systematic characterization of the polymeric precursors and the corresponding graphene nanoribbons in terms of structural and electronic properties, and we compute the Raman and infrared spectra. The band structure properties are examined by considering the bonding features and the partial charge densities of the structures. The physical origin of the infrared and Raman peaks is investigated in terms of the morphology and vibrational properties of the precursors and products. We show that light spectroscopy provides a unique fingerprint for each type of GNR, which may be used to monitor the quality of the final products and the kinetics of the synthesis process.

Homogeneous ice nucleation from supercooled water was studied in the temperature range of 220-240 K through combining the forward flux sampling method (Allen et al., J. Chem. Phys., 2006, 124, 024102) with molecular dynamics simulations (FFS/MD), based on a recently developed coarse-grained water model (mW) (Molinero et al., J. Phys. Chem. B, 2009, 113, 4008). The calculated ice nucleation rates display a strong temperature dependence, ranging from 2.148 ± 0.635 × 10(25) m(-3) s(-1) at 220 K to 1.672 ± 0.970 × 10(-7) m(-3) s(-1) at 240 K. These rates can be fitted according to the classical nucleation theory, yielding an estimate of the effective ice-water interface energy γ(ls) of 31.01 ± 0.21 mJ m(-2) for the mW water model. Compared to experiments, our calculation underestimates the homogeneous ice nucleation rate by a few orders of magnitude. Possible reasons for the discrepancy are discussed. The nucleating ice embryo contains both cubic ice Ic and hexagonal ice Ih, with the fraction of each structure being roughly 50% when the critical size is reached. In particular, a novel defect structure containing nearly five-fold twin boundaries is identified in the ice clusters formed during nucleation. The way such defect structure is formed is found to be different from mechanisms proposed for the formation of the same defect in metallic nanoparticles and thin film. The quasi five-fold twin boundary structure found here is expected to occur in the crystallization of a wide range of materials with the diamond cubic structure, including ice.

Using molecular dynamics simulations, we show that the thermal conductivity (κ) of Si(0.5)Ge(0.5) can be reduced by more than one order of magnitude by etching nanometer-sized holes in the material, and it becomes almost constant as a function of temperature between 300 and 1100 K for samples with 1 nm wide pores. In nanoporous SiGe, thermal conduction is largely determined by mass disorder and boundary scattering, and thus the dependence of κ on pore distance and on structural, atomistic disorder is much weaker than in the case of nanoporous Si. This indicates that one may minimize κ of the alloy with less stringent morphological constraints than for pure Si.

We show that first principles hybrid functional (PBE0) simulations of the infrared spectrum of liquid water yields a much better agreement with experimental results than a semilocal functional description; in particular, the quantitative accord with measured stretching and bending bands is very good. Such an improved description stems from two effects: a more accurate account, at the PBE0 level of theory, of the vibrational properties of the monomer and dimer and an underlying structural model for the liquid with a smaller number of hydrogen bonds and oxygen coordination than those obtained with semilocal functionals. The average electronic gap of the liquid is increased by 60% with respect to the PBE value, when computed at the PBE0 level of theory, and is in fair agreement with experimental results.

We present molecular and lattice dynamics calculations of the thermal conductivity of nanoporous silicon, and we show that it may attain values 10-20 times smaller than in bulk Si for porosities and surface-to-volume ratios similar to those obtained in recently fabricated nanomeshes. Further reduction of almost an order of magnitude is obtained in thin films with thickness of 20 nm, in agreement with experiment. We show that the presence of pores has two main effects on heat carriers: appearance of non-propagating, diffusive modes and reduction of the group velocity of propagating modes. The former effect is enhanced by the presence of disorder at the pore surfaces, while the latter is enhanced by decreasing film thickness.

Chronic myeloid leukemia (CML) patients treated with imatinib develop frequent resistance generally due to a point mutation. Recently, large rearrangements of abl sequence have also been described. In this study, we focused on the complete deletion of exon 7. We screened for bcr-abl(delexon7) in 63 resistant patients by high-resolution melting (HRM) analysis and direct sequencing. Moreover, we analyzed expression of abl(delexon7) and bcr-abl(delexon7) in 17 CML patients at diagnosis, 32 patients at resistance, and 20 negative controls by quantitative PCR or fragment length analysis. bcr-abl(delexon7) was detected on 34 (54%) among 63 resistant patients by HRM, showing an increase in the sensitivity of screening, because only 3.2% could be detected by direct sequencing. This deletion was not associated with a point mutation (P = 0.3362). In addition, abl(delexon7) was found in all tested samples with the same pattern of expression, suggesting an alternative splicing mechanism. In the bcr-abl component, there was no statistical difference between CML patients at diagnosis and resistant patients (P = 0.2815) as regarding bcr-abl(delexon7) proportion, thus arguing against involvement of deletion in resistance. Moreover, among two patients harboring bcr-abl(delexon7) at diagnosis, one experienced a complete disappearance of this transcript, and the other decreased >75% at resistance. In conclusion, bcr-abl(delexon7) is frequently observed in CML patients when using sensitive techniques. It seems to be the result of an alternative splicing mechanism and to be independent from the occurrence of resistance., (©2010 AACR.)

We have investigated the process of rehydroxylation of pyrophyllite as a limiting factor to the dehydroxylation upon thermal treatment. Car-Parrinello molecular dynamics simulations based on density functional theory have been used along with the metadynamics algorithm. Two possible rehydroxylation mechanisms reaction have been characterized, related to two possible intermediate structures along the rehydroxylation paths, and both involve the interaction of the apical oxygen atoms. At high temperature, the rehydroxylation reaction is highly competitive (free energy barrier (DeltaF) = 1.5 kcal/mol) and inhibits the progress of the dehydroxylation reaction (DeltaF = 40 kcal/mol). In addition to the rehydroxylation of the dehydroxylated structure, the water molecule supports the interconversion of the cross and on-site intermediates as well. Thus, rehydroxylation and interconversion among intermediates can justify the wide range of transformations as a function of the temperature observed experimentally.

We compute the lattice thermal conductivity (kappa) of silicon nanowires as a function of temperature by molecular dynamics simulations. In wires with amorphous surfaces kappa may reach values close to that of amorphous silicon and is nearly constant between 200 and 600 K; this behavior is determined by the presence of a majority of nonpropagating vibrational modes. We develop a parameter-free model that accounts for the temperature dependence observed in our simulations and provides a qualitative explanation of recent experiments.

The early stages of crystallization of tetrahedral systems remain largely unknown, due to experimental limitations in spatial and temporal resolutions. Computer simulations, when combined with advanced sampling techniques, can provide valuable details about nucleation at the atomistic level. Here we describe a computational approach that combines the forward flux sampling method with molecular dynamics, and we apply it to the study of nucleation in supercooled liquid silicon. We investigated different supercooling temperatures, namely, 0.79, 0.86, and 0.95 of the equilibrium melting point T(m). Our results show the calculated nucleation rates decrease from 5.52+/-1.75x10(28) to 4.77+/-3.26x10(11) m(-3) s(-1) at 0.79 and 0.86 T(m), respectively. A comparison between simulation results and those of classical nucleation theory shows that the free energy of the liquid solid interface gamma(ls) inferred from our computations differ by about 28% from that obtained for bulk liquid solid interfaces. However the computed values of gamma(ls) appear to be rather insensitive to supercooling temperature variations. Our simulations also yield atomistic details of the nucleation process, including the atomic structure of critical nuclei and lifetime distributions of subcritical nuclei.

Surfaces have long been known to have an intricate role in solid-liquid phase transformations. Whereas melting is often observed to originate at surfaces, freezing usually starts in the bulk, and only a few systems have been reported to exhibit signatures of surface-induced crystallization. These include assembly of chain-like molecules, some liquid metals and alloys and silicate glasses. Here, we report direct computational evidence of surface-induced nucleation in supercooled liquid silicon and germanium, and we illustrate the crucial role of free surfaces in the freezing process of tetrahedral liquids exhibiting a negative slope of their melting lines (dT/dP|coexist<0). Our molecular dynamics simulations show that the presence of free surfaces may enhance the nucleation rates by several orders of magnitude with respect to those found in the bulk. Our findings provide insight, at the atomistic level, into the nucleation mechanism of widely used semiconductors, and support the hypothesis of surface-induced crystallization in other tetrahedrally coordinated systems, in particular water in the atmosphere.

We present a series of molecular dynamics, lattice dynamics, and Boltzmann transport equation calculations aimed at understanding heat transport in Silicon nanowires. In agreement with recent experiments, we find that the computed thermal conductivity strongly depends on the surface structure. It may be as high as that of bulk Si for crystalline wires, while wires with amorphous surfaces have the smallest thermal conductivity, about 100 times lower than the bulk. Two, combined effects are responsible for this dramatic difference: the presence, at disordered surfaces, of extended, nonpropagating modes analogous to heat carriers in amorphous Si, together with decreased lifetimes of propagating modes.

We present computer simulations of liquid and solid phases of condensed methane at pressures below 25 GPa, between 150 and 300 K, where no appreciable molecular dissociation occurs. We used molecular dynamics (MD) and metadynamics techniques and empirical potentials in the rigid molecule approximation, whose validity was confirmed a posteriori by carrying out ab initio MD simulations for selected pressure and temperature conditions. Our results for the melting line are in satisfactory agreement with existing measurements. We find that the fcc crystal transforms into a hcp structure with four molecules per unit cell (B phase) at about 10 GPa and 150 K, and that the B phase transforms into a monoclinic high pressure phase above 20 GPa. Our results for solid/solid phase transitions are consistent with those of Raman studies but the phase boundaries estimated in our calculations are at higher pressure than those inferred from spectroscopic data.

We compare calculations of infrared (IR) spectra of water confined between nonpolar surfaces, obtained by molecular dynamics simulations with forces either computed using density functional theory or modeled by empirical potentials. Our study allows for the identification of important electronic effects, contributing to IR signals, that are not included in simulations based on empirical force fields, and cannot be extracted from the analysis of vibrational density of states. These effects originate from electronic charge fluctuations involving both surface and water molecules in close proximity of the interface. The implications of our findings for the interpretation of experimental data are discussed.

We have computed infrared (IR) spectra of water confined between nonpolar surfaces by using ab initio calculations. We show that electronic charge fluctuations at the interface, occurring even in the case of highly hydrophobic substrates, are responsible for specific features present in IR signals and for important differences between IR spectra and vibrational density of states. We also find that most of the frequency shifts observed under confinement originate from the modified hydrogen bonded network in close proximity to the interface.

We delineate the dehydroxylation reaction of pyrophyllite in detail by localizing the complete reaction path on the free energy surface obtained previously by Car-Parrinello molecular dynamics and the implemented metadynamics algorithm ( Molina-Montes et al. J. Phys. Chem. B 2008, 112, 7051 ). All intermediates were identified, and a transition state search was also undertaken with the PRFO algorithm. The characterization of this reaction and the atomic rearrangement in the intermediates and products at quantum mechanical level were performed for the two reaction paths found previously: (i) direct dehydroxylation through the octahedral hole (cross mechanism) or between contiguous hydroxyl groups (on-site mechanism) and (ii) two-step dehydroxylation assisted by apical oxygens for each of the two steps. New intermediates were found and determined structurally. The structural variations found for all intermediates and transition states are in agreement with experimental results. The formation of these structures indicates that the dehydroxylation process is much more complex than a first-order reaction and can explain the wide range of temperatures for completing the reaction, and these results can be extrapolated to the dehydroxylation of other dioctahedral 2:1 phyllosilicates.

The dehydroxylation of pyrophyllite involves the reaction of OH groups and elimination of water molecules through two possible mechanisms, one involving the bridging hydroxyl groups of an octahedral Al (3+) pair and the other two hydroxyl groups reacting across the dioctahedral vacancy. First-principles molecular dynamics simulations at the density functional theory level are used together with the metadynamics algorithm to explore the free-energy surface (FES) of the initial step of the dehydroxylation. We observe that the two possible dehydroxylation mechanisms yield similar activation energies at 0 K, but at high temperatures, the cross mechanism has lower free energy than that of the on-site one. The dehydroxylation process produces different semidehydroxylated intermediates that should be taken into account. The role of the temperature in favoring a dehydroxylation nonconcerted chain mechanism over another is here elucidated, and a novel competitive mechanism, which is assisted by the structural apical oxygens in the high-temperature regime, is proposed.