Integrating Newton's equations of motion in the reciprocal space.

We here present the normal dynamics technique, which recasts the Newton's equations of motion in terms of phonon normal modes by exploiting a proper sampling of the reciprocal space. After introducing the theoretical background, we discuss how the reciprocal space sampling enables us to (i) obtain a computational speedup by selecting which and how many wave vectors of the Brillouin zone will be considered and (ii) account for distortions realized across large atomic distances without the use of large simulation cells. We implemented the approach into an open-source code, which we used to present three case studies: in the first one, we elucidate the general strategy for the sampling of the reciprocal space; in the second one, we illustrate the potential of the approach by studying the stabilization effect of temperature in α-uranium; and in the last one, we investigate the characterization of Raman spectra at different temperatures in MoS2/MX2 transition metal dichalcogenide heterostructures. Finally, we discuss how the procedure is general and can be used to simulate periodic, semiperiodic, and finite systems such as crystals, slabs, nanoclusters, or molecules.

Effect of different anticoagulants and antiplatelets on intraoral bleeding time during professional oral hygiene session.

OBJECTIVE: Patients with thromboembolic problems, prosthetic valves, or coagulation issues are commonly prescribed anticoagulants and antiplatelets. Anticoagulant and antiplatelet medication might constitute a challenge for dentists and dental hygienists since possible prolonged bleeding might interfere with dental procedures. The aim of the present study was to examine the bleeding durations associated with various anticoagulants and antiplatelets during professional dental hygiene sessions, utilizing a modified Ivy test adapted for the oral context. MATERIALS AND METHODS: Ninety-three consecutive patients undergoing professional oral hygiene were recruited. Debridement during oral hygiene was performed using ultrasonic mechanical instrumentation, and bleeding sites were assessed and treated with gentle pressure using sterile gauzes. The time for bleeding cessation was recorded. Patients were categorized into six groups based on their drug intake, Control: no anticoagulants or antiplatelets DTI: direct thrombin inhibitors (dabigatran) AntiXa: directa factor Xa inhibitors (endoxaban, apixaban, rivaroxaban) VKA: vitamin K antagonists (warfarin, acenocoumarol) SAPT: single anti-platelet therapy (acetylsalicylic acid or clopidogrel) DAPT: dual anti-platelet therapy (acetylsalicylic acid and clopidogrel). Bleeding time was measured in seconds and mean values were assessed among the different groups. Differences between groups were investigated with Kruskal-Wallis test followed by Dunn's post-hoc correction for multiple comparisons or two-way ANOVA followed by Dunnett post-hoc; RESULTS: Control patients presented the lowest bleeding time 50 s, followed by AntiXa (98), SAPT (105), DTI (120), DAPT (190) and VKA (203). A statistically significant difference was present among control and DTI (p = 0.004), VKA (p < 0.001), DAPT (p < 0.001). CONCLUSIONS: Based on the present outcomes, an increased risk of prolonged bleeding emerged in patients taking VKA and DAPT. CLINICAL SIGNIFICANCE: bleeding did not interfere with the oral hygiene session The optimal period for dental treatment of these patients should be 2-3 h before the next dose, without the need to temporarily suspend the medication.

UItra-low friction and edge-pinning effect in large-lattice-mismatch van der Waals heterostructures.

Two-dimensional heterostructures are excellent platforms to realize twist-angle-independent ultra-low friction due to their weak interlayer van der Waals interactions and natural lattice mismatch. However, for finite-size interfaces, the effect of domain edges on the friction process remains unclear. Here we report the superlubricity phenomenon and the edge-pinning effect at MoS2/graphite and MoS2/hexagonal boron nitride van der Waals heterostructure interfaces. We found that the friction coefficients of these heterostructures are below 10-6. Molecular dynamics simulations corroborate the experiments, which highlights the contribution of edges and interface steps to friction forces. Our experiments and simulations provide more information on the sliding mechanism of finite low-dimensional structures, which is vital to understand the friction process of laminar solid lubricants.

Viewpoint: Atomic-Scale Design Protocols toward Energy, Electronic, Catalysis, and Sensing Applications.

Nanostructured materials are essential building blocks for the fabrication of new devices for energy harvesting/storage, sensing, catalysis, magnetic, and optoelectronic applications. However, because of the increase of technological needs, it is essential to identify new functional materials and improve the properties of existing ones. The objective of this Viewpoint is to examine the state of the art of atomic-scale simulative and experimental protocols aimed to the design of novel functional nanostructured materials, and to present new perspectives in the relative fields. This is the result of the debates of Symposium I "Atomic-scale design protocols towards energy, electronic, catalysis, and sensing applications", which took place within the 2018 European Materials Research Society fall meeting.

Features in chemical kinetics. III. Attracting subspaces in a hyper-spherical representation of the reactive system.

In this work, we deal with general reactive systems involving N species and M elementary reactions under applicability of the mass-action law. Starting from the dynamic variables introduced in two previous works [P. Nicolini and D. Frezzato, J. Chem. Phys. 138(23), 234101 (2013); 138(23), 234102 (2013)], we turn to a new representation in which the system state is specified in a (N × M)(2)-dimensional space by a point whose coordinates have physical dimension of inverse-of-time. By adopting hyper-spherical coordinates (a set of dimensionless "angular" variables and a single "radial" one with physical dimension of inverse-of-time) and by examining the properties of their evolution law both formally and numerically on model kinetic schemes, we show that the system evolves towards the equilibrium as being attracted by a sequence of fixed subspaces (one at a time) each associated with a compact domain of the concentration space. Thus, we point out that also for general non-linear kinetics there exist fixed "objects" on the global scale, although they are conceived in such an abstract and extended space. Moreover, we propose a link between the persistence of the belonging of a trajectory to such subspaces and the closeness to the slow manifold which would be perceived by looking at the bundling of the trajectories in the concentration space.

Computational Design of Photosensitive Polymer Templates To Drive Molecular Nanofabrication.

Molecular electronics promises the ultimate level of miniaturization of computers and other machines as organic molecules are the smallest known physical objects with nontrivial structure and function. But despite the plethora of molecular switches, memories, and motors developed during the almost 50-years long history of molecular electronics, mass production of molecular computers is still an elusive goal. This is mostly due to the lack of scalable nanofabrication methods capable of rapidly producing complex structures (similar to silicon chips or living cells) with atomic precision and a small number of defects. Living nature solves this problem by using linear polymer templates encoding large volumes of structural information into sequence of hydrogen bonded end groups which can be efficiently replicated and which can drive assembly of other molecular components into complex supramolecular structures. In this paper, we propose a nanofabrication method based on a class of photosensitive polymers inspired by these natural principles, which can operate in concert with UV photolithography used for fabrication of current microelectronic processors. We believe that such a method will enable a smooth transition from silicon toward molecular nanoelectronics and photonics. To demonstrate its feasibility, we performed a computational screening of candidate molecules that can selectively bind and therefore allow the deterministic assembly of molecular components. In the process, we unearthed trends and design principles applicable beyond the immediate scope of our proposed nanofabrication method, e.g., to biologically relevant DNA analogues and molecular recognition within hydrogen-bonded systems.

Toward quantitative estimates of binding affinities for protein-ligand systems involving large inhibitor compounds: a steered molecular dynamics simulation route.

Understanding binding mechanisms between enzymes and potential inhibitors and quantifying protein-ligand affinities in terms of binding free energy is of primary importance in drug design studies. In this respect, several approaches based on molecular dynamics simulations, often combined with docking techniques, have been exploited to investigate the physicochemical properties of complexes of pharmaceutical interest. Even if the geometric properties of a modeled protein-ligand complex can be well predicted by computational methods, it is still challenging to rank with chemical accuracy a series of ligand analogues in a consistent way. In this article, we face this issue calculating relative binding free energies of a focal adhesion kinase, an important target for the development of anticancer drugs, with pyrrolopyrimidine-based ligands having different inhibitory power. To this aim, we employ steered molecular dynamics simulations combined with nonequilibrium work theorems for free energy calculations. This technique proves very powerful when a series of ligand analogues is considered, allowing one to tackle estimation of protein-ligand relative binding free energies in a reasonable time. In our cases, the calculated binding affinities are comparable with those recovered from experiments by exploiting the Michaelis-Menten mechanism with a competitive inhibitor.

Features in chemical kinetics. I. Signatures of self-emerging dimensional reduction from a general format of the evolution law.

Simplification of chemical kinetics description through dimensional reduction is particularly important to achieve an accurate numerical treatment of complex reacting systems, especially when stiff kinetics are considered and a comprehensive picture of the evolving system is required. To this aim several tools have been proposed in the past decades, such as sensitivity analysis, lumping approaches, and exploitation of time scales separation. In addition, there are methods based on the existence of the so-called slow manifolds, which are hyper-surfaces of lower dimension than the one of the whole phase-space and in whose neighborhood the slow evolution occurs after an initial fast transient. On the other hand, all tools contain to some extent a degree of subjectivity which seems to be irremovable. With reference to macroscopic and spatially homogeneous reacting systems under isothermal conditions, in this work we shall adopt a phenomenological approach to let self-emerge the dimensional reduction from the mathematical structure of the evolution law. By transforming the original system of polynomial differential equations, which describes the chemical evolution, into a universal quadratic format, and making a direct inspection of the high-order time-derivatives of the new dynamic variables, we then formulate a conjecture which leads to the concept of an "attractiveness" region in the phase-space where a well-defined state-dependent rate function ω has the simple evolution ω[over dot]=-ω(2) along any trajectory up to the stationary state. This constitutes, by itself, a drastic dimensional reduction from a system of N-dimensional equations (being N the number of chemical species) to a one-dimensional and universal evolution law for such a characteristic rate. Step-by-step numerical inspections on model kinetic schemes are presented. In the companion paper [P. Nicolini and D. Frezzato, J. Chem. Phys. 138, 234102 (2013)] this outcome will be naturally related to the appearance (and hence, to the definition) of the slow manifolds.

Features in chemical kinetics. II. A self-emerging definition of slow manifolds.

In the preceding paper of this series (Part I [P. Nicolini and D. Frezzato, J. Chem. Phys. 138, 234101 (2013)]) we have unveiled some ubiquitous features encoded in the systems of polynomial differential equations normally applied in the description of homogeneous and isothermal chemical kinetics (mass-action law). Here we proceed by investigating a deeply related feature: the appearance of so-called slow manifolds (SMs) which are low-dimensional hyper-surfaces in the neighborhood of which the slow evolution of the reacting system occurs after an initial fast transient. Indeed a geometrical definition of SM, devoid of subjectivity, "naturally" follows in terms of a specific sub-dimensional domain embedded in the peculiar region of the concentrations phase-space that in Part I we termed as "attractiveness region." Numerical inspections on simple low-dimensional model cases are presented, including the benchmark case of Davis and Skodje [J. Chem. Phys. 111, 859 (1999)] and the preliminary analysis of a simplified model mechanism of hydrogen combustion.

Shortcomings of the standard Lennard-Jones dispersion term in water models, studied with force matching.

In this work, ab initio parametrization of water force field is used to get insights into the functional form of empirical potentials to properly model the physics underlying dispersion interactions. We exploited the force matching algorithm to fit the interaction forces obtained with dispersion corrected density functional theory based molecular dynamics simulations. We found that the standard Lennard-Jones interaction potentials poorly reproduce the attractive character of dispersion forces. This drawback can be resolved by accounting for the distinctive short range behavior of dispersion interactions, multiplying the r(-6) term by a damping function. We propose two novel parametrizations of the force field using different damping functions. Structural and dynamical properties of the new models are computed and compared with the ones obtained from the non-damped force field, showing an improved agreement with reference first principle calculations.

Twisting Dynamics of Large Lattice-Mismatch van der Waals Heterostructures.

van der Waals (vdW) homo/heterostructures are ideal systems for studying interfacial tribological properties such as structural superlubricity. Previous studies concentrated on the mechanism of translational motion in vdW interfaces. However, detailed mechanisms and general properties of the rotational motion are barely explored. Here, we combine experiments and simulations to reveal the twisting dynamics of the MoS2/graphite heterostructure. Unlike the translational friction falling into the superlubricity regime with no twist angle dependence, the dynamic rotational resistances highly depend on twist angles. Our results show that the periodic rotational resistance force originates from structural potential energy changes during the twisting. The structural potential energy of MoS2/graphite heterostructure increases monotonically from 0° to 30° twist angles, and the estimated relative energy barrier is (1.43 ± 0.36) × 10-3 J/m2. The formation of Moiré superstructures in the graphene layer is the key to controlling the structural potential energy of the MoS2/graphene heterostructure. Our results suggest that in twisting 2D heterostructures, even if the interface sliding friction is negligible, the evolving potential energy change results in a nonvanishing rotational resistance force. The structural change of the heterostructure can be an additional pathway for energy dissipation in the rotational motion, further enhancing the rotational friction force.

Exploring Nanoscale Lubrication Mechanisms of Multilayer MoS2 During Sliding: The Effect of Humidity.

Solid lubricants have received substantial attention due to their excellent frictional properties. Among others, molybdenum disulfide (MoS2) is one of the most studied lubricants. Humidity results in a deterioration of the frictional properties of MoS2. The actual mechanism at the nanoscale is still under debate, although there are indications that chemical reactions are not likely to occur in defect-free structures. In this study, we performed nonequilibrium molecular dynamics simulations to study the frictional properties of multilayer MoS2 during sliding in the presence of water. Moreover, we also investigated the effect of sliding speed and normal load. We confirmed earlier results that a thin layer of water organizes as a solidified, ice-like network of hydrogen bonds as a result of being confined in a two-dimensional fashion between MoS2. Moreover, we found that there exists an energy-driven, rotational dependence of the water network atop/beneath MoS2. This orientational anisotropy is directly related to the dissipative character of MoS2 during sliding. Finally, three distinct frictional regimes were identified, two for a thin layer of water and one for bulk water. In the case of a thin layer and low coverage, water represents a solid-like contaminant, causing high energy dissipation. For a thin layer and high coverage, water starts to act as a solid-like lubricant, reducing dissipation during sliding. Finally, a regime where water acts as a liquid lubricant, characterized by a clear velocity dependence was found.

Exploring the Stability of Twisted van der Waals Heterostructures.

Recent research showed that the rotational degree of freedom in stacking 2D materials yields great changes in the electronic properties. Here, we focus on an often overlooked question: are twisted geometries stable and what defines their rotational energy landscape? Our simulations show how epitaxy theory breaks down in these systems, and we explain the observed behavior in terms of an interplay between flexural phonons and the interlayer coupling, governed by the moiré superlattice. Our argument, applied to the well-studied MoS2/graphene system, rationalizes experimental results and could serve as guidance to design twistronic devices.

Structural Ordering of Molybdenum Disulfide Studied via Reactive Molecular Dynamics Simulations.

Molybdenum disulfide (MoS2) is a well-known and effective lubricant that provides extremely low values of coefficient of friction. It is known that the sliding process may induce structural transformations of amorphous or disordered MoS2 to the crystalline phase with basal planes oriented parallel to the sliding direction, which is optimal for reducing friction. However, the key reaction parameters and conditions promoting this structural transformation are still largely unknown. We investigate, by employing reactive molecular dynamics simulations, the formation of MoS2 layers from an amorphous phase as a function of temperature, initial sample density, and sliding velocity. We show that the formation of ordered crystalline structures can be explained in the framework of classical nucleation theory as it predicts the conditions for their nucleation and growth. These results may have important implications in the fields of coating and thin-film deposition, tribology, and in all technological applications where a fast and effective structural transition to an ordered phase is needed.

On the lubricity of transition metal dichalcogenides: an ab initio study.

Owing to specific characteristics engendered by their lamellar structures, transition metal dichalcogenides are posited as being some of the best dry lubricants available. Herein, we report a density functional investigation into the sliding properties and associated phenomena of these materials. Calculated potential energy and charge transfer profiles are used to highlight the dependence of shear strength on chemical composition and bilayer orientation (sliding direction). Furthermore, our calculations underscore the intrinsic relationship between incommensurate crystals and the oft-touted superlubric behaviour of molybdenum disulfide.

Exploiting Configurational Freezing in Nonequilibrium Monte Carlo Simulations.

To achieve acceptable accuracy in fast-switching free energy estimates by Jarzynski equality [ Phys. Rev. Lett. 1997 , 78 , 2690 ] or Crooks fluctuation theorem [ J. Stat. Phys. 1998 , 90 , 1481 ], it is often necessary to realize a large number of externally driven trajectories. This is basically due to inefficient calculation of path-ensemble averages arising from the work dissipated during the nonequilibrium paths. We propose a computational technique, addressed to Monte Carlo simulations, to improve free energy estimates by lowering the dissipated work. The method is inspired by the dynamical freezing approach, recently developed in the context of molecular dynamics simulations [ Phys. Rev. E 2009 , 80 , 041124 ]. The idea is to limit the configurational sampling to particles of a well-established region of the sample (namely, the region where dissipation is supposed to occur), while leaving fixed (frozen) the other particles. Therefore, the method, called configurational freezing, is based on the reasonable assumption that dissipation is a local phenomenon in single-molecule nonequilibrium processes, a statement which is satisfied by most processes, including folding of biopolymers, molecular docking, alchemical transformations, etc. At variance with standard simulations, in configurational freezing simulations the computational cost is not correlated with the size of the whole system, but rather with that of the reaction site. The method is illustrated in two examples, i.e., the calculation of the water to methane relative hydration free energy and the calculation of the potential of mean force of two methane molecules in water solution as a function of their distance.

Hummer and Szabo-like potential of mean force estimator for bidirectional nonequilibrium pulling experiments/simulations.

In the framework of single-molecule pulling experiments, the system is typically driven out of equilibrium by a time-dependent external potential V(t) acting on a collective coordinate such that the total Hamiltonian is the sum of V(t) and the Hamiltonian in the absence of external perturbation. Nonequilibrium work theorems such as Jarzynski equality and Crooks fluctuation theorem have been devised to recover free energy differences between states of this extended system. However, one is often more interested in the potential of mean force of the unperturbed Hamiltonian, i.e., in the effective potential dictating the equilibrium distribution of the collective coordinate in the absence of the external potential. In this respect, Hummer and Szabo proposed an algorithm to estimate the desired free energy differences when pulling experiments are performed in only one direction of the process ( Proc. Natl. Acad. Sci. USA 2001, 98, 3658 ). In this paper, we present a potential of mean force estimator of the unperturbed system that exploits the work measured in both forward and backward directions of the process. The method is based on the reweighting technique of Hummer and Szabo and on the Bennett acceptance ratio. Using Brownian-dynamics simulations on a double-well free energy surface, we show that the estimator works satisfactorily in any pulling situation, from nearly equilibrium to strongly dissipative regimes. The method is also applied to the unfolding/refolding process of decaalanine, a system vastly used to illustrate and to test nonequilibrium methodologies. A thorough comparative analysis with another bidirectional potential of mean force estimator ( Minh, D. D. L.; Adib, A. B. Phys. Rev. Lett. 2008, 100, 180602 ) is also presented. The proposed approach is well-suited to recover free energy profiles from single-molecule bidirectional-pulling experiments such as those performed by optical tweezers or atomic force microscopes.

Improving fast-switching free energy estimates by dynamical freezing.

An important limitation of nonequilibrium pulling experiments/simulations in recovering free energy differences is the poor convergence of path-ensemble averages. Therefore, a large number of fast-switching trajectories needs to achieve free energy estimates with acceptable accuracy. We propose a method to improve free energy estimates by drastically lowering the computational cost of steered molecular dynamics simulations employed to realize such trajectories. This is accomplished by generating trajectories where the particles not directly involved in the driven process are dynamically frozen. Such a freezing is dynamical rather than thermal because it is reached by a synchronous scaling of atomic masses and velocities keeping the kinetic energy of each particle unchanged. The forces between dynamically frozen particles can then be calculated rarely. Thus, it is possible to generate realizations of a process whose computational cost is not correlated with the size of the whole system, but only with that of the reaction site. The method is illustrated on a simple model system and its general applicability is discussed.