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The potential energy landscape (PEL) formalism is a tool within statistical mechanics that has been used in the past to calculate the equation of states (EOS) of classical rigid model liquids at low temperatures, where computer simulations may be challenging. In this work, we use classical molecular dynamics (MD) simulations and the PEL formalism to calculate the EOS of the flexible q-TIP4P/F water model. This model exhibits a liquid–liquid critical point (LLCP) in the supercooled regime, at (Pc = 150 MPa, Tc = 190 K, and ρc = 1.04 g/cm3) [using the reaction field technique]. The PEL-EOS of q-TIP4P/F water and the corresponding location of the LLCP are in very good agreement with the MD simulations. We show that the PEL of q-TIP4P/F water is Gaussian, which allows us to calculate the configurational entropy of the system, Sconf. The Sconf of q-TIP4P/F water is surprisingly similar to that reported previously for rigid water models, suggesting that intramolecular flexibility does not necessarily add roughness to the PEL. We also show that the Adam–Gibbs relation, which relates the diffusion coefficient D with Sconf, holds for the flexible q-TIP4P/F water model. Overall, our results indicate that the PEL formalism can be used to study molecular systems that include molecular flexibility, the common case in standard force fields. This is not trivial since the introduction of large bending/stretching mode frequencies is problematic in classical statistical mechanics. For example, as shown previously, we find that such high frequencies lead to unphysical (negative) entropy for q-TIP4P/F water when using classical statistical mechanics (yet, the PEL formalism can be applied successfully). [ABSTRACT FROM AUTHOR]

We perform path integral molecular dynamics (PIMD) simulations of a monatomic liquid that exhibits a liquid–liquid phase transition and liquid–liquid critical point. PIMD simulations are performed using different values of Planck's constant h, allowing us to study the behavior of the liquid as nuclear quantum effects (NQE, i.e., atoms delocalization) are introduced, from the classical liquid (h = 0) to increasingly quantum liquids (h > 0). By combining the PIMD simulations with the ring-polymer molecular dynamics method, we also explore the dynamics of the classical and quantum liquids. We find that (i) the glass transition temperature of the low-density liquid (LDL) is anomalous, i.e., T g LDL (P) decreases upon compression. Instead, (ii) the glass transition temperature of the high-density liquid (HDL) is normal, i.e., T g HDL (P) increases upon compression. (iii) NQE shift both T g LDL (P) and T g HDL (P) toward lower temperatures, but NQE are more pronounced on HDL. We also study the glass behavior of the ring-polymer systems associated with the quantum liquids studied (via the path-integral formulation of statistical mechanics). There are two glass states in all the systems studied, low-density amorphous ice (LDA) and high-density amorphous ice (HDA), which are the glass counterparts of LDL and HDL. In all cases, the pressure-induced LDA–HDA transformation is sharp, reminiscent of a first-order phase transition. In the low-quantum regime, the LDA–HDA transformation is reversible, with identical LDA forms before compression and after decompression. However, in the high-quantum regime, the atoms become more delocalized in the final LDA than in the initial LDA, raising questions on the reversibility of the LDA–HDA transformation. [ABSTRACT FROM AUTHOR]

Owing to their atomic thickness and low bending rigidity, suspended two-dimensional (2D) materials are prone to wrinkle formation. Here, we use molecular dynamics (MD) simulations to probe the effect of these wrinkles on the nonlinear elasticity of atomically thin graphene membranes. We observe a stress–strain response that consists of two linear regions that are separated by a transition. It is found that this transition is sharp in membranes where wrinkles are formed by uneven stresses at the boundaries. However, when wrinkles are formed by crystal defects, this nonlinear transition is seen to be more gradual. To capture these effects, we use a phenomenological model based on experimentally measurable quantities. We demonstrate the model's fidelity by fitting it to the MD simulated nonlinear response of many graphene membranes providing evidence that the sharpness of the transition between the linear regions in the stress–strain response is a measure of the type of wrinkles and can be quantified by our model. [ABSTRACT FROM AUTHOR]

Heat transfer between a silver nanoparticle and surrounding water has been studied using molecular dynamics (MD) simulations. The thermal conductance (Kapitza conductance) at the interface between a nanoparticle and surrounding water has been calculated using four different approaches: transient with/without temperature gradient (internal thermal resistance) in the nanoparticle, steady-state non-equilibrium, and finally equilibrium simulations. The results of steady-state non-equilibrium and equilibrium are in agreement but differ from the transient approach results. MD simulation results also reveal that in the quenching process of a hot silver nanoparticle, heat dissipates into the solvent over a length-scale of ∼2 nm and over a time scale of less than 5 ps. By introducing a continuum solid-like model and considering a heat conduction mechanism in water, it is observed that the results of the temperature distribution for water shells around the nanoparticle agree well with the MD results. It is also found that the local water thermal conductivity around the nanoparticle is greater by about 50% than that of bulk water. These results have important implications for understanding heat transfer mechanisms in nanofluid systems and also for cancer photothermal therapy, wherein an accurate local description of heat transfer in an aqueous environment is crucial. [ABSTRACT FROM AUTHOR]

To investigate the chemical isotope-exchange reactions within a system composed of a mixture of hydrogen and deuterium (H/D) in the plasma media, the ReaxFFHD potential was parameterized against an appropriate quantum mechanics (QM)-based training set. These QM data involve structures and energies related to bond dissociation, angle distortion, and an exchange reaction of the tri-atomic molecular ions, H3+, D3+, H2D+, and D2H+, produced in the hydrogen plasma. Using the ReaxFFHD potential, a range of reactive molecular dynamics simulations were performed on different mixtures of H/D systems. Analysis of the reactions involved in the production of these tri-atomic molecular ions was carried out over 1 ns simulations. The results show that the ReaxFFHD potential can properly model isotope-exchange reactions of tri-atomic molecular ions and that it also has a perfect transferability to reactions taking place in these systems. In our simulations, we observed some intermediate molecules (H2, D2, and HD) that undergo secondary reactions to form the tri-atomic molecular ions as the most likely products in the hydrogen plasma. Moreover, there remains a preference for D in the produced molecular ions, which is related to the lower zero-point energy of the D-enriched species, showing the isotope effects at the heart of the ReaxFFHD potential. [ABSTRACT FROM AUTHOR]

Poly-glycine-alanine (poly-GA) proteins are widely believed to be one of the main toxic dipeptide repeat molecules associated with amyotrophic lateral sclerosis (ALS) and frontotemporal dementia diseases. Using discontinuous molecular dynamics simulation and an all-atom model of the proteins, we study folding, stability, and aggregation of poly-GA. The results demonstrate that poly-GA is an aggregation-prone protein that, after a long enough time, forms β-sheet-rich aggregates that match recent experiment data and that two unique helical structures are formed very frequently, namely, β-helix and double-helix. The details of the two structures are analyzed. The analysis indicates that such helical structures are stable and share the characteristics of both α-helices and β-sheets. Molecular simulations indicate that identical phenomena also occur in the aggregation of poly-glycine-arginine (poly-GR). Therefore, we hypothesize that proteins of type (GX)n in which X may be any non-glycine amino acid and n is the repeat length may share the same folding structures of β-helix and double-helix and that it is the glycine in the repeat that contributes the most to this characteristic. Molecular dynamics simulation with continuous interaction potentials and explicit water molecules as the solvent supports the hypothesis. To our knowledge, this is the first molecular dynamics simulation of the phenomena involving poly-GA and poly-GR proteins. [ABSTRACT FROM AUTHOR]

Amorphous TiO2 (a-TiO2) could offer an attractive alternative to conventional crystalline TiO2 phases for photocatalytic applications. However, the atomic structure of a-TiO2 remains poorly understood with respect to that of its crystalline counterparts. Here, we conduct some classical molecular dynamics simulations of a-TiO2 based on a selection of empirical potentials. We show that, on account of its ability to dynamically assign the charge of each atom based on its local environment, the secondmoment tight-binding charge equilibration potential yields an unprecedented agreement with available experimental data. Based on these simulations, we investigate the degree of order and disorder in a-TiO2. Overall, the results suggest that a-TiO2 features a large flexibility in its local topology, which may explain the high sensitivity of its structure to the synthesis method being used. [ABSTRACT FROM AUTHOR]

Transport of saltwater through pristine and positively charged single-layer graphene nanoporous membranes is investigated using molecular dynamics simulations. Pressure-driven flows are induced by motion of specular reflecting boundaries at feed and permeate sides with constant speed. Unlike previous studies in the literature, this method induces a desired flow rate and calculates the resulting pressure difference in the reservoirs. Due to the hexagonal structure of graphene, the hydraulic diameters of nano-pores are used to correlate flow rate and pressure drop data. Simulations are performed for three different pore sizes and flow rates for the pristine and charged membrane cases. In order to create better statistical averages for salt rejection rates, ten different initial conditions of Na+ and Cl− distribution in the feed side are used for each simulation case. Using data from 180 distinct simulation cases and utilizing the Buckingham Pi theorem, we develop a functional relationship between the volumetric flow rate, pressure drop, pore diameter, and the dynamic viscosity of saltwater. A linear relationship between the volumetric flow rate and pressure drop is observed. For the same flow rate and pore size, charged membranes exhibit larger pressure drops. Graphene membranes with 9.90 Å pore diameter results in 100% salt rejection with 163.2 l/h cm2 water flux, requiring a pressure drop of 35.02 MPa. [ABSTRACT FROM AUTHOR]

We develop a computationally efficient and methodologically simple approach to realize molecular dynamics simulations of electrodeposition. Our minimal model takes into account the nontrivial electric field due a sharp electrode tip to perform simulations of the controllable coating of a thin layer on a surface with an atomic precision. On the atomic scale a highly site-selective electrodeposition of ions and charged particles by means of the sharp tip of a scanning probe microscope is possible. A better understanding of the microscopic process, obtained mainly from atomistic simulations, helps us to enhance the quality of this nanopatterning technique and to make it applicable in fabrication of nanowires and nanocontacts. In the limit of screened inter-particle interactions, it is feasible to run very fast simulations of the electrodeposition process within the framework of the proposed model and thus to investigate how the shape of the overlayer depends on the tip-sample geometry and dielectric properties, electrolyte viscosity, etc. Our calculation results reveal that the sharpness of the profile of a nano-scale deposited overlayer is dictated by the normal-to-sample surface component of the electric field underneath the tip. [ABSTRACT FROM AUTHOR]

We study effective two- and three-body interactions between non-active colloidal inclusions in an active bath of chiral or non-chiral particles, using Brownian dynamics simulations within a standard, two-dimensional model of disk-shaped inclusions and active particles. In a non-chiral active bath, we first corroborate previous findings on effective two-body repulsion mediated between the inclusions by elucidating the detailed non-monotonic features of the two-body force profiles, including a primary maximum and a secondary hump at larger separations that was not previously reported. We then show that these features arise directly from the formation, and sequential overlaps, of circular layers (or "rings") of active particles around the inclusions, as the latter are brought to small surface separations. These rings extend to radial distances of a few active-particle radii from the surface of inclusions, giving the hard-core inclusions relatively thick, soft, repulsive "shoulders," whose multiple overlaps then enable significant (non-pairwise) three-body forces in both non-chiral and chiral active baths. The resulting three-body forces can even exceed the two-body forces in magnitude and display distinct repulsive and attractive regimes at intermediate to large self-propulsion strengths. In a chiral active bath, we show that, while active particles still tend to accumulate at the immediate vicinity of the inclusions, they exhibit strong depletion from the intervening region between the inclusions and partial depletion from relatively thick, circular zones further away from the inclusions. In this case, the effective, predominantly repulsive interactions between the inclusions turn to active, chiralityinduced, depletion-type attractions, acting over an extended range of separations. [ABSTRACT FROM AUTHOR]

The magnitude of the pH of the surface of water continues to be a contentious topic in the physical chemistry of aqueous interfaces. Recent theoretical studies have shown little or no preference for the proton to be at the surface compared to the bulk. Using ab initio molecular dynamics simulations, we revisit the propensity of the excess proton for the air-water interface with a particular focus on the role of instantaneous liquid interfaces. We find a more pronounced presence for the proton to be at the air-water interface. The enhanced water structuring around the proton results in the presence of proton wires that run parallel to the surface as well as a hydrophobic environment made up of undercoordinated topological defect water molecules, both of which create favorable conditions for proton confinement at the surface. The Grotthuss mechanism within the structured water layer involves a mixture of both concerted and closely spaced stepwise proton hops. The proton makes excursions within the first solvation layer either in proximity to or along the instantaneous interface. [ABSTRACT FROM AUTHOR]

Ellipticine is a natural product that is currently being actively investigated for its inhibitory cancer and HIV properties. Here we use path-integral molecular dynamics coupled with excited state calculations to characterize the role of nuclear quantum effects on the structural and electronic properties of ellipticine in water, a common biological solvent. Quantum effects collectively enhance the fluctuations of both light and heavy nuclei of the covalent and hydrogen bonds in ellipticine. In particular, for the ellipticine-water system, where the proton donor and acceptor have different proton affinities, we find that nuclear quantum effects (NQEs) strengthen both the strong and the weak H bonds. This is in contrast to what is observed for the cases where the proton affinity of the donors and acceptors is same. These structural fluctuations cause a significant red-shift in the absorption spectra and an increase in the broadening, bringing it into closer agreement with the experiments. Our work shows that nuclear quantum effects alter both qualitatively and quantitatively the optical properties of this biologically relevant system and highlights the importance of the inclusion of these effects in the microscopic understanding of their optical properties. We propose that isotopic substitution will produce a blue shift and a reduction in the broadening of the absorption peak. [ABSTRACT FROM AUTHOR]

In this work, we use ab initio molecular dynamics coupled with metadynamics to explore and characterize the glassy potential energy landscape of the OH- in a 20 and 48 water cluster. The structural, energetic, and topological properties of OH- are characterized for both clusters and the molecular origins of the IR signatures are examined. We find that in both the small and large clusters, the OH- can donate or accept a varying number of hydrogen bonds confirming that the amphiphilic character does not depend on cluster size. However, we highlight some important differences found between the energetic and topological properties of both families of clusters which may have implications on understanding the changes in the solvation structure of OH- between bulk and interfacial environments. By studying the IR spectra of smaller subsets of molecules within the 20 water molecule cluster, we find that the IR spectrum of the bare OH- as well as the water molecule donating a strong hydrogen bond to it exhibits characteristic absorption along the amphiphilic band between 1500 and 3000 cm-1 at positions very similar to those found for the entire hydroxide cluster. The results presented here will be useful in the calibration and improvement of both ab initio and semi-empirical methods to model this complex anion. [ABSTRACT FROM AUTHOR]

Molecular dynamics simulations are carried out to study the translational and rotational diffusion of a single Janus particle immersed in a dense Lennard-Jones fluid. We consider a spherical particle with two hemispheres of different wettabilities. The analysis of the particle dynamics is based on the time-dependent orientation tensor, particle displacement, as well as the translational and angular velocity autocorrelation functions. It was found that both translational and rotational diffusion coefficients increase with decreasing surface energy at the nonwetting hemisphere, provided that the wettability of the other hemisphere remains unchanged. We also observed that in contrast to homogeneous particles, the nonwetting hemisphere of the Janus particle tends to rotate in the direction of the displacement vector during the rotational relaxation time. [ABSTRACT FROM AUTHOR]

We analyze van der Waals interactions between two rigid polymers with sequence-specific, anisotropic polarizabilities along the polymer backbones, so that the dipole moments fluctuate parallel to the polymer backbones. Assuming that each polymer has a quenched-in polarizability sequence which reflects, for example, the polynucleotide sequence of a double-stranded DNA molecule, we study the van derWaals interaction energy between a pair of such polymers with rod-like structure for the cases where their respective polarizability sequences are (i) distinct and (ii) identical, with both zero and non-zero correlation length of the polarizability correlator along the polymer backbones in the latter case. For identical polymers, we find a novel r-5 scaling behavior of the van der Waals interaction energy for small inter-polymer separation r, in contradistinction to the r-4 scaling behavior of distinct polymers, with furthermore a pronounced angular dependence favoring attraction between sufficiently aligned identical polymers. Such behavior can assist the molecular recognition between polymers. [ABSTRACT FROM AUTHOR]

Using classical molecular dynamics simulations, we investigate the dielectric properties at interfaces of water with graphene, graphite, hexane, and water vapor. For graphite, we compare metallic and nonmetallic versions. At the vapor–liquid water and hexane–water interfaces, the laterally averaged dielectric profiles are significantly broadened due to interfacial roughness and only slightly anisotropic. In contrast, at the rigid graphene surface, the dielectric profiles are strongly anisotropic and the perpendicular dielectric profile exhibits pronounced oscillations and sign changes. The interfacial dielectric excess, characterized by the shift of the dielectric dividing surface with respect to the Gibbs dividing surface, is positive for all surfaces, showing that water has an enhanced dielectric response at hydrophobic surfaces. The dielectric dividing surface positions vary significantly among the different surfaces, which points to pronounced surface-specific dielectric behavior. The interfacial repulsion of a chloride ion is shown to be dominated by electrostatic interactions for the soft fluid–fluid interfaces and by non-electrostatic Lennard-Jones interactions for the rigid graphene–water interface. A linear tensorial dielectric model for the ion–interface interaction with sharp dielectric interfaces located on the dielectric dividing surface positions works well for graphene but fails for vapor and hexane, because these interfaces are smeared out. The repulsion of chloride from the metallic and nonmetallic graphite versions differs very little, which reflects the almost identical interfacial water structure and can be understood based on linear continuum dielectric theory. Interface flexibility shows up mostly in the nonlinear Coulomb part of the ion–interface interaction, which changes significantly close to the interfaces and signals the breakdown of linear dielectric continuum theory. [ABSTRACT FROM AUTHOR]

The crossing of a transition state in a multidimensional reactive system is mediated by invariant geometric objects in phase space: An invariant hyper-sphere that represents the transition state itself and invariant hyper-cylinders that channel the system towards and away from the transition state. The existence of these structures can only be guaranteed if the invariant hyper-sphere is normally hyperbolic, i.e., the dynamics within the transition state is not too strongly chaotic. We study the dynamics within the transition state for the hydrogen exchange reaction in three degrees of freedom. As the energy increases, the dynamics within the transition state becomes increasingly chaotic. We find that the transition state first looses and then, surprisingly, regains its normal hyperbolicity. The important phase space structures of transition state theory will, therefore, exist at most energies above the threshold. [ABSTRACT FROM AUTHOR]

The Stokes–Einstein (S–E) relation is well studied for pure liquids. Here, we report the applicability of the S–E relation in liquid mixtures. The breakdown of the S–E relation in organic and aqueous liquid mixtures might be attributed to the self-diffusion coefficient, shear viscosity, or the hydrodynamics radius of the solute–solvent species, which are strongly correlated. The hydrodynamic radius must be adjusted with an effective radius that accounts for the size of the diffusing solute wetted by the solvent molecules. Furthermore, the mutual diffusivity could be the correct option instead of self-diffusivity for the prediction of hydrodynamic radius using the S–E relation, as the mobility of the solute is strongly coupled with the mobility of the solvent molecules. The theoretical hydrodynamic radius obtained from the S–E relation is predicted to be well correlated with the distance between the solute and solvent center of mass calculated from molecular dynamics simulations. The acceptance of this effective hydrodynamic radius is ensured by testing its applicability for a large collection of liquid mixtures. [ABSTRACT FROM AUTHOR]

We prove that interfacial asperity sharpness allows for tuning superlattice in-plane thermal conductivity below or above the limit of high roughness derived from the Lucas-Ziman (LZ) model. Whereas LZ's model predicts molecular dynamic (MD) results of Lennard-Jones superlattices for small asperities, it has to be modified with a roughness- and sharpness-dependent layer thickness to remain relevant at higher roughness. For the case of sharpest asperities, the modified LZ model still fails, and ray-tracing computations matching MD data reveal a phonon-trap effect in the asperity valleys. This behavior scales with the Knudsen number and should appear at the micron scale in large mean-free-path crystals, such as silicon. [ABSTRACT FROM AUTHOR]

This study reveals the essence of ligand recognition mechanisms by which calmodulin (CaM) controls a variety of Ca2+ signaling processes. We study eight forms of calcium-loaded CaM each with distinct conformational states. Reducing the structure to two degrees of freedom conveniently describes main features of the conformational changes of CaM via simultaneous twist-bend motions of the two lobes. We utilize perturbation-response scanning (PRS) technique, coupled with molecular dynamics simulations. PRS is based on linear response theory, comprising sequential application of directed forces on selected residues followed by recording the resulting protein coordinates. We analyze directional preferences of the perturbations and resulting conformational changes. Manipulation of a single residue reproduces the structural change more effectively than that of single/pairs/triplets of collective modes of motion. Our findings also give information on how the flexible linker acts as a transducer of binding information to distant parts of the protein. Furthermore, by perturbing residue E31 located in one of the EF hand motifs in a specific direction, it is possible to induce conformational change relevant to five target structures. Independently, using four different pKa calculation strategies, we find this particular residue to be the charged residue (out of a total of 52), whose ionization state is most sensitive to subtle pH variations in the physiological range. It is plausible that at relatively low pH, CaM structure is less flexible. By gaining charged states at specific sites at a pH value around 7, such as E31 found in the present study, local conformational changes in the protein will lead to shifts in the energy landscape, paving the way to other conformational states. These findings are in accordance with Fluorescence Resonance Energy Transfer (FRET) measured shifts in conformational distributions towards more compact forms with decreased pH. They also corroborate mutational studies and proteolysis results which point to the significant role of E31 in CaM dynamics. [ABSTRACT FROM AUTHOR]

We, theoretically, investigate the effect of ions on the packing and ejection dynamics of flexible and semiflexible polymers from spherical viral capsids. We find that when the polymer charge is less screened, or the Debye length increases (corresponding to a buffer with low concentration of a monovalent salt, such as Na+), the packing becomes more difficult and it may stop midway. Ejection, instead, proceeds more easily if the electrostatic screening is small. On the other hand, more screening (corresponding, for example, to the addition of divalent ions such as Mg2 +) results in easier packing and slower ejection. We interpret this as resulting from electrostatic forces among the various polymer sections, which can be tuned with the type of salt present in the solution. We also discuss how the DNA structure inside the capsid changes due to screened electrostatic interactions. [ABSTRACT FROM AUTHOR]

A scheme is described for performing molecular dynamics simulations on polymers under nonperiodic, stochastic boundary conditions. It has been designed to allow later the embedding of a particle domain treated by molecular dynamics into a continuum environment treated by finite elements. It combines, in the boundary region, harmonically restrained particles to confine the system with dissipative particle dynamics to dissipate energy and to thermostat the simulation. The equilibrium position of the tethered particles, the so-called anchor points, are well suited for transmitting deformations, forces and force derivatives between the particle and continuum domains. In the present work the particle scheme is tested by comparing results for coarse-grained polystyrene melts under nonperiodic and regular periodic boundary conditions. Excellent agreement is found for thermodynamic, structural, and dynamic properties. [ABSTRACT FROM AUTHOR]

The crystallization of nitromethane, CH3NO2, from the melt on the (100), (010), (001), and (110) crystal surfaces at 170, 180, 190, 200, 210, and 220 K has been investigated using constant-volume and -temperature (NVT) molecular dynamics simulations with a realistic, fully flexible force field [D. C. Sorescu, B. M. Rice, and D. L. Thompson, J. Phys. Chem. B 104, 8406 (2000)]. The crystallization process and the nature of the solid-liquid interface have been investigated by computing the molecular orientations, density, and radial distribution functions as functions of time and location in the simulation cell. During crystallization the translational motion of the molecules ceases first, after which molecular rotation ceases as the molecules assume proper orientations in the crystal lattice. The methyl groups are hindered rotors in the liquid; hindrance to rotation is reduced upon crystallization. The width of the solid-liquid interface varies between 6 and 13 Å (about two to five molecular layers) depending on which crystal surface is exposed to the melt and which order parameter is used to define the interface. The maximum rate of crystallization varies from 0.08 molecules ns-1 Å-2 for the (010) surface at 190 K to 0.41 molecules ns-1 Å-2 for the (001) surface at 220 K. [ABSTRACT FROM AUTHOR]

We derive the mode spectrum of the thermal boundary resistance between two bodies having a temperature difference ΔT. A general expression of the time τ that defines the resistance is derived as the equilibrium autocorrelation of ΔT integrated over time. A further decomposition of this autocorrelation yields the resistance spectrum as equal to the mode relaxation time weighted by its energy mean square fluctuation. We then perform molecular dynamics simulations of argon like crystals in equilibrium and nonequilibrium regimes to prove the relevance of our model. This general method allows for deriving the resistance spectrum and therefore can yield key rules to control the exchanged heat flux. [ABSTRACT FROM AUTHOR]

The quantum-classical Liouville equation provides a description of the dynamics of a quantum subsystem coupled to a classical environment. Representing this equation in the mapping basis leads to a continuous description of discrete quantum states of the subsystem and may provide an alternate route to the construction of simulation schemes. In the mapping basis the quantum-classical Liouville equation consists of a Poisson bracket contribution and a more complex term. By transforming the evolution equation, term-by-term, back to the subsystem basis, the complex term (excess coupling term) is identified as being due to a fraction of the back reaction of the quantum subsystem on its environment. A simple approximation to quantum-classical Liouville dynamics in the mapping basis is obtained by retaining only the Poisson bracket contribution. This approximate mapping form of the quantum-classical Liouville equation can be simulated easily by Newtonian trajectories. We provide an analysis of the effects of neglecting the presence of the excess coupling term on the expectation values of various types of observables. Calculations are carried out on nonadiabatic population and quantum coherence dynamics for curve crossing models. For these observables, the effects of the excess coupling term enter indirectly in the computation and good estimates are obtained with the simplified propagation. [ABSTRACT FROM AUTHOR]

A study of the structural relaxation of nitromethane subsequent to shock loading normal to the (100) crystal plane performed using molecular dynamics and a nonreactive potential was reported recently [J. Chem. Phys. 131, 064503 (2009)]. Starting from initial temperatures of T0=50 and 200 K, shocks were simulated using impact velocities Up ranging from 0.5 to 3.0 km s-1; clear evidence of melting was obtained for shocks initiated with impacts of 2.0 km s-1 and higher. Here, we report the results of analyses of those simulation data using a method based on the Eckart frame normal-mode analysis that allows partitioning of the kinetic energy among the molecular degrees of freedom. A description of the energy transfer is obtained in terms of average translational and rotational kinetic energies in addition to the rates of individual vibrational mode heating. Generally, at early times postshock a large superheating of the translational and rotational degrees of freedom (corresponding to phonon modes of the crystal) is observed. The lowest frequency vibrations (gateway modes) are rapidly excited and also exhibit superheating. Excitation of the remaining vibrational modes occurs more slowly. A rapid, early excitation of the symmetric C–H stretch mode was observed for the shock conditions T0=50 K and Up=2.0 km s-1 due to a combination of favorable alignment of molecular orientation with the shock direction and frequency matching between the vibration and shock velocity. [ABSTRACT FROM AUTHOR]

Molecules subjected to shock waves will, in general, undergo significant intramolecular distortion and exhibit large amplitude orientational and translational displacements relative to the unshocked material. The analysis of molecular dynamics simulations of strongly perturbed materials is complicated, particularly when the goal is to express time-dependent molecular-scale properties in terms of structural or geometric descriptors/properties defined for molecules in the equilibrium geometry. We illustrate the use of the Eckart–Sayvetz condition in a molecular dynamics study of the response of crystalline nitromethane subjected to supported shock waves propagating normal to (100). The simulations were performed with the nonreactive but vibrationally accurate force field due to Sorescu et al. [J. Phys. Chem. B 104, 8406 (2000)]. Shocks were initiated with impact velocities of Up=0.5, 1.0, 2.0, and 3.0 km s-1 in crystals at initial temperatures of T0=50 and 200 K. Statistical precision in the analysis was enhanced through the use of a spatiotemporal reference frame centered on the advancing shock front, which was located as a function of time using the gradient of the kinetic energy along the shock direction. The Eckart–Sayvetz condition provides a rigorous approach by which the alignment can be obtained between a coordinate frame for a perturbed molecule and one in a convenient reference frame (e.g., one based on the equilibrium crystal structure) for analyses of the molecules in the material as the system evolves toward equilibrium. Structural and dynamic properties of the material corresponding to orientation in the lattice, translational symmetry, and mass transport (orientational order parameters, two dimensional radial distribution functions, and self-diffusion coefficients, respectively) were computed as functions of time with 4 fs resolution. The results provide clear evidence of melting for shocks initiated by impacts of at least Up=2.0 km s-1 and provide insights into the evolution of changes at the molecular-mode level associated with the onset of the melting instability in shocked crystal. [ABSTRACT FROM AUTHOR]

We use coarse-grained molecular dynamics simulations to perform tensile test deformation on glassy and rubbery polymer samples using two types of driving for the deformation. We compare the outcome from a standard homogeneous deformation procedure with that of a boundary driven procedure in which the sample is driven by the nanometric equivalent of grips. No significant difference is observed in both uniaxial and triaxial tensile experiments. Implications for testing the behavior of nonhomogeneous polymer materials are briefly discussed. [ABSTRACT FROM AUTHOR]

Heat conduction between parallel plates separated by a thin layer of liquid Argon is investigated using three-dimensional molecular dynamics (MD) simulations employing 6-12 Lennard-Jones potential interactions. Channel walls are maintained at specific temperatures using a recently developed interactive thermal wall model. Heat flux and temperature distribution in nanochannels are calculated for channel heights varying from 12.96 to 3.24 nm. Fourier law of heat conduction is verified for the smallest channel, while the thermal conductivity obtained from Fourier law is verified using the predictions of Green-Kubo theory. Temperature jumps at the liquid/solid interface, corresponding to the well known Kapitza resistance, are observed. Using systematic studies thermal resistance length at the interface is characterized as a function of the surface wettability, thermal oscillation frequency, wall temperature, thermal gradient, and channel height. An empirical model for the thermal resistance length, which could be used as the jump coefficient of a Navier boundary condition, is developed. Temperature distribution in nanochannels is predicted using analytical solution of continuum heat conduction equation subjected to the new temperature jump condition. Analytical predictions are verified using MD simulations. [ABSTRACT FROM AUTHOR]

The melting of nitromethane initiated at solid-vacuum interfaces has been investigated using molecular dynamics nvt simulations with a realistic force field [D. C. Sorescu et al., J. Phys. Chem. B 104, 8406 (2000)]. The calculated melting point (251±5 K) is in good agreement with experiment (244.73 K) and values obtained previously (∼255.5 and 266.5±8 K) using other simulation methods [P. M. Agrawal et al., J. Chem. Phys. 119, 9617 (2003)]. Analyses of the molecular orientations and diffusion during the simulations as functions of the distance from the exposed surfaces show that the melting is a direct crystal-to-liquid transition, in which the molecules first gain rotational freedom, then mobility. There is a slight dependence of the melting temperature on the exposed crystallographic face. [ABSTRACT FROM AUTHOR]

A scaling law relating the shear viscosity of one and two component liquid mixtures to their excess thermodynamic entropies defined through pair correlation functions is derived by approximating the mode coupling theory expressions of frictions and then combining with the Stokes-Einstein relation. Molecular dynamics simulation has been performed to generate the data of shear viscosity for one and two component liquid mixtures to test the derived scaling law. The derived scaling laws yield numerical results of shear viscosity for one component and two component liquid mixtures, which are in excellent agreement with the molecular dynamics simulation results for a wide range of density and interaction potential. [ABSTRACT FROM AUTHOR]

Using a novel experimental protocol involving second harmonic generation (SHG), the rotational, reorientation dynamics of disperse red 1 (DR1) chromophores doped at 2 wt. % in polystyrene (PS) have been monitored over 11 decades in time, from 10-6 s onwards. This nonlinear optical (NLO) technique allows quantification of the average rotational, reorientation time constant 〈τ〉 over a broad range of temperatures, 28 to 138 °C, above and below the glass transition temperature Tg. Good agreement was obtained between 〈τ〉’s determined from SHG and dielectric relaxation measurements. This is expected since both SHG and dielectric relaxation measurements of PS+2 wt. % DR1 monitor the rotational reorientation of DR1 chromophores. Values of 〈τ〉 fit well to a Williams–Landel–Ferry equation above Tg, indicating that the rotational reorientation of DR1 is coupled to the α relaxation of PS; below Tg the values of 〈τ〉 show an apparent Arrhenius temperature dependence with an activation energy of 45–50 kcal/mol. Above Tg, the SHG data are in agreement with the literature values of the temperature dependence of the α-relaxation dynamics for homopolymer PS obtained using NMR, viscosity, compliance, and photon correlation spectroscopy measurements; at Tg the absolute values of 〈τ〉 obtained by SHG are also in good agreement with the literature values obtained for relaxation times in PS using NMR, photon correlation spectroscopy, and enthalpy relaxation. Upon scaling the data using a reduced parameter, Tr/T, where Tr is close to the calorimetrically determined Tg, an excellent overlap of SHG results for the rotational reorientation dynamics of DR1 and thereby the α transition in PS, poly(ethyl methacrylate), and poly(isobutyl methacrylate) is observed below Tg; however, above Tg, the PS data show a much stronger temperature dependence, suggesting that PS may be a more ‘‘fragile’’... [ABSTRACT FROM AUTHOR]

Presents a study which discussed an activation analysis of the nucleation of a half-square dislocation loop from the tip of a tensile crack. Stress and thermal softening effects obtained by molecular dynamics; Nucleation of a dislocation loop by the Rice-Thomson model; Nonlinear stress distribution; Examination of the effect of anisotropic elasticity in the study of dislocation nucleation.

Presents a study that modeled a Carnot-like irreversible power cycle with isothermal and adiabatic, irreversible processes. Comparison between the performances of the irreversible power cycle and those of the endoreversible cycle; Influence of internal irreversibilities in general; Formulation of the maximum power and maximum efficiency objectives.

Graphene and several other two-dimensional (2D) carbon-based structures, including C3N, C3B, C2N, C3N4 (s-triazine), and C3N4 (tri-triazine), have attracted considerable attention due to their excellent thermal, mechanical, and electrical properties. In this study, the correlations between the interfacial thermal conductance (ITC) across these 2D nanostructures and the lattice-dynamical properties of the system, including (i) the phonon density of state (DOS) overlap between the sides of the interface and (ii) the percentage of different classes of vibrational modes for each heterostructure, are investigated. The results show that the percentage of localized interfacial modes is a strong descriptor for predicting ITC—even more effective than the widely accepted phonon DOS overlap. Moreover, the ITC between all combinations of these six carbon-based materials, its dependence on the length of the heterostructure, and the thermal rectification effect present in each interface structure is studied using non-equilibrium molecular dynamics simulations. The results show that the maximum and minimum ITC for infinite length systems belong to graphene/C3N and C2N/C3N4 (tri-triazine) heterostructures with values of 35.81 and 2.21 GW m−2 K−1, respectively. Comparing the thermal resistances at the interface and in the bulk of these heterostructures show that thermal transport in carbon-based 2D materials is influenced by the thermal resistance across their interfaces. These results not only contribute to our fundamental understanding of interfacial heat transfer, but can also serve as the basis for the design of nanoelectronic devices based on 2D materials, where the device level performance will indeed be influenced by interfacial phenomena. [ABSTRACT FROM AUTHOR]

Van der Waals heterostructures have exhibited interesting physical properties. In this paper, heat transfer in hybrid coplanar bilayer/monolayer (BL-ML) graphene, as a model layered van der Waals heterostructure, was studied using non-equilibrium molecular dynamics (MD) simulations. The temperature profile and inter- and intra-layer heat fluxes of the BL-ML graphene indicated that, there is no fully developed thermal equilibrium between layers and the drop in the average temperature profile at the step-like BL-ML interface is not attributable to the effect of Kapitza resistance. By increasing the length of the system up to 1 μm in the studied MD simulations, the thermally non-equilibrium region was reduced to a small area near the step-like interface. All MD results were compared to a continuum model and a good match was observed between the two approaches. Our results provide a useful understanding of heat transfer in nano- and micro-scale layered materials and van der Waals heterostructures. [ABSTRACT FROM AUTHOR]

Whether it is glass, ceramics, cement, or concrete, minimizing thermal conduction through disordered materials is a determining factor when it comes to reducing the energy consumption of cities. In this work, we explore underlying physical processes involved in thermal conduction through the disordered glue of cement, calcium-silicate-hydrates (CSH). We find that at 300 K, phonon-like propagating modes in accordance with the Boltzmann transport theory, propagons, account for more than 30% of the total thermal conductivity, while diffusons, described via the Allen-Feldman theory, contribute to the remainder. The cumulative thermal conductivity proves to be close to both equilibrium molecular dynamics calculations and experimental values. These findings help us establish different strategies, such as localization schemes (to weaken diffusons) and scattering mechanisms (to constrain propagons), for reduction of thermal conductivity of CSH without sacrificing its mechanical properties. [ABSTRACT FROM AUTHOR]

In this paper we investigate the fluid transport inside a single-wall carbon nanotube induced by a temperature gradient along the tube length, focusing on the effect of fluid-wall interaction strength. It is found that the fluid moves from the hot side of the nanotube towards the cold side. By increasing the fluid-wall interaction strength, the fluid volumetric flux assumes a maximum, increases, and then decreases. Fluid transport is pressure-driven in weak interactions; in contrast, in strong interactions, the fluid is broken into two parts in the radial direction. Fluid transport in the central regions of the tube is pressure-driven, while it is surface-driven in the areas close to the wall. [ABSTRACT FROM AUTHOR]

Tri-isoamyl phosphate (TiAP) has been proposed to be an alternative for tri-butyl phosphate (TBP) in the Plutonium Uranium Extraction (PUREX) process. Recently, we have successfully calibrated and tested all-atom optimized potentials for liquid simulations using Mulliken partial charges for pure TiAP, TBP, and dodecane by performing molecular dynamics (MD) simulation. It is of immense importance to extend this potential for the various molecular properties of TiAP and TiAP/n-dodecane binary mixtures using MD simulation. Earlier, efforts were devoted to find out a suitable force field which can explain both structural and dynamical properties by empirical parameterization. Therefore, the present MD study reports the structural, dynamical, and thermodynamical properties with different mole fractions of TiAP-dodecane mixtures at the entire range of mole fraction of 0–1 employing our calibrated Mulliken embedded optimized potentials for liquid simulation (OPLS) force field. The calculated electric dipole moment of TiAP was seen to be almost unaffected by the TiAP concentration in the dodecane diluent. The calculated liquid densities of the TiAP-dodecane mixture are in good agreement with the experimental data. The mixture densities at different temperatures are also studied which was found to be reduced with temperature as expected. The plot of diffusivities for TiAP and dodecane against mole fraction in the binary mixture intersects at a composition in the range of 25%-30% of TiAP in dodecane, which is very much closer to the TBP/n-dodecane composition used in the PUREX process. The excess volume of mixing was found to be positive for the entire range of mole fraction and the excess enthalpy of mixing was shown to be endothermic for the TBP/n-dodecane mixture as well as TiAP/n-dodecane mixture as reported experimentally. The spatial pair correlation functions are evaluated between TiAP–TiAP and TiAP–dodecane molecules. Further, shear viscosity has been computed by performing the non-equilibrium molecular dynamics employing the periodic perturbation method. The calculated shear viscosity of the binary mixture is found to be in excellent agreement with the experimental values. The use of the newly calibrated OPLS force field embedding Mulliken charges is shown to be equally reliable in predicting the structural and dynamical properties for the mixture without incorporating any arbitrary scaling in the force field or Lennard-Jones parameters. Further, the present MD simulation results demonstrate that the Stokes-Einstein relation breaks down at the molecular level. The present methodology might be adopted to evaluate the liquid state properties of an aqueous-organic biphasic system, which is of great significance in the interfacial science and technology. [ABSTRACT FROM AUTHOR]

The investigation of devitrification in thermally annealed nanodimensional glassy alloy thin films provides a comprehensive understanding of their thermal stability, which can be used to explore potential applications. The amorphous to crystalline polymorphous transformation of cosputtered Ni-Zr alloy (Ni78Zr22 at. %) films, with a thickness lower than the reported critical limit of devitrification, was studied through detailed structural characterization and molecular dynamics (MD) simulations. Devitrification to a nanocrystalline state (Ni7Zr2 structure) was observed at 800 °C, with an increase in density (∼3.6%) much higher than that achieved in bulk alloys. Variation in the magnetic property of the films and the overall physical structure including morphology and composition were examined before and after annealing. MD simulations were employed to effectively elucidate not only the high densification but also the increased magnetic moment after annealing, which was correlated with the simulated change in the coordination number around Ni atoms. The structural relaxation process accompanying devitrification was described as a disorder-to-order transformation while highlighting the crucial role played by chemical short range order prevalent in glassy materials. [ABSTRACT FROM AUTHOR]

Most previous studies on gas transport in nano-scale confinements assume dynamic similarity with rarefied gas flows, and employ kinetic theory based models. This approach is incomplete, since it neglects the van der Waals forces imposed on gas molecules by the surfaces. Using three-dimensional molecular dynamics (MD) simulations of force driven gas flows, we show the significance of wall force field in nano-scale confinements by defining a new dimensionless parameter (B) as the ratio of the wall force-penetration length to the channel height. Investigation of gas transport in different nano-channels at various Knudsen numbers show the importance of wall force field for finite B values, where the dynamic similarity between the rarefied and nano-scale gas flows break down. Comparison of MD results employing molecularly structured three-dimensional walls versus reflection of gas molecules from a two-dimensional planar surface with Maxwell distribution show that the nano-confinement effects cannot be resolved by the latter approach, frequently used in kinetic theory calculations. Molecularly structured walls determine the bulk flow physics by setting a proper tangential momentum accommodation coefficient, and they also determine the transport in the near wall region. Gas nano-flows with finite B exhibit significant differences in the local density and velocity profiles, affecting the mass flow rate and the formation of Knudsen's minimum in nano-channels. [ABSTRACT FROM AUTHOR]

A reply by the authors of the article "Correlated electron-nuclear dynamics: Exact factorization of the molecular wavefunction,'' to comments within the issue by J. L. Alonso, J. Clemente-Gallardo, P. Echenique-Robba, and J. A. Jover-Galtier is presented. A mathematical proof that norms of electronic and nuclear waveforms are preserved by time evolution which uses Lagrange multipliers is offered.

This study combines molecular dynamics (MD) simulations with small angle x-ray scattering (SAXS) measurements to investigate the range of conformations that can be adopted by a pH/ionic strength (IS) sensitive protein and to quantify its distinct populations in solution. To explore how the conformational distribution of proteins may be modified in the environmental niches of biological media, we focus on the periplasmic ferric binding protein A (FbpA) from Haemophilus influenzae involved in the mechanism by which bacteria capture iron from higher organisms. We examine iron-binding/release mechanisms of FbpA in varying conditions simulating its biological environment. While we show that these changes fall within the detectable range for SAXS as evidenced by differences observed in the theoretical scattering patterns calculated from the crystal structure models of apo and holo forms, detection of conformational changes due to the point mutation D52A and changes in ionic strength (IS) from SAXS scattering profiles have been challenging. Here, to reach conclusions, statistical analyses with SAXS profiles and results from different techniques were combined in a complementary fashion. The SAXS data complemented by size exclusion chromatography point to multiple and/or alternative conformations at physiological IS, whereas they are well-explained by single crystallographic structures in low IS buffers. By fitting the SAXS data with unique conformations sampled by a series of MD simulations under conditions mimicking the buffers, we quantify the populations of the occupied substates. We also find that the D52A mutant that we predicted by coarse-grained computational modeling to allosterically control the iron binding site in FbpA, responds to the environmental changes in our experiments with conformational selection scenarios that differ from those of the wild type. [ABSTRACT FROM AUTHOR]

In this work, we use ab initio molecular dynamics simulations to elucidate the electronic properties of three hydrated zwitterionic amino acids, namely proline, hydroxyproline, and alanine, the former two forming an important constituent of collagen. In all three systems, we find a substantial amount of charge transfer between the amino acids and surrounding solvent, which, rather surprisingly, also involves the reorganization of electron density near the hydrophobic non-polar groups. Water around proline appears to be slightly more polarized, as reflected by the enhanced water dipole moment in its hydration shell. This observation is also complemented by an examination of the IR spectra of the three systems where there is a subtle red and blue shift in the O–H stretch and bend regions, respectively, for proline. We show that polarizability of these amino acids as revealed by a dipole moment analysis involves a significant enhancement from the solvent and that this also involves non-polar groups. Our results suggest that quantum mechanical effects are likely to be important in understanding the coupling between biomolecules and water in general and in hydrophobic interactions. [ABSTRACT FROM AUTHOR]

Motivated by electrowetting-based flow control in nano-systems, water transport in graphene nanochannels is investigated as a function of the applied electric field. Molecular dynamics simulations are performed for deionized water confined in graphene nano-channels subjected to opposing surface charges, creating an electric field across the channel. Water molecules respond to the electric field by reorientation of their dipoles. Oxygen and hydrogen atoms in water face the anode and cathode, respectively, and hydrogen atoms get closer to the cathode compared to the oxygen atoms near the anode. These effects create asymmetric density distributions that increase with the applied electric field. Force-driven water flows under electric fields exhibit asymmetric velocity profiles and unequal slip lengths. Apparent viscosity of water increases and the slip length decreases with increased electric field, reducing the flow rate. Increasing the electric field above a threshold value freezes water at room temperature. [ABSTRACT FROM AUTHOR]