Water droplets on rugged hydrophobic surfaces typically exhibit one of the following two states: ( i ) Wenzel state [Wenzel RN (1936) Ind Eng Chem 28:988–994] in which water are full contact with surface (referred as wetted contact) or ii Cassie [Cassie, ABD, Baxter S (1944) Trans Faraday Soc 40:546–551] peaks well “air pockets” trapped between grooves (the composite contact). Here, we show large-scale molecular dynamics simulation transition and a periodic nanopillared surface. Physical...

Position and orientation of water protons need to be specified when the molecular simulation studies are performed for clathrate hydrates. Positions oxygen atoms in experimentally determined by X-ray diffraction analysis hydrate structures, but positions hydrogen lattice disordered. This study reports a determination proton coordinates unit cell structure I (sI), II (sII), H (sH) hydrates that satisfy ice rules, have lowest potential energy configuration protons, give net zero dipole moment....

Molecular dynamics computer simulation was carried out to investigate the of vapor phase homogeneous nucleation at triple point temperature under supersaturation ratio 6.8 for a Lennard-Jones fluid. To control system temperature, 5000 target particles were mixed with soft-core carrier gas particles. The observed rate is seven orders magnitude larger than prediction classical theory. kinetically defined critical nucleus size, which growth and decay rates are balanced, 30–40, as large...

We perform large-scale molecular dynamics simulations to measure the contact-angle hysteresis for a nanodroplet of water placed on nanopillared surface. The droplet can be in either Cassie state (droplet being top surface) or Wenzel contact with bottom nanopillar grooves). To quantitative fashion, simulation is designed such that number molecules droplets systematically varied, but base nanopillars are direct fixed. find weaker than state. This conclusion consistent experimental observation....

Reservoir computing is a temporal information processing system that exploits artificial or physical dissipative dynamics to learn dynamical and generate the target time-series. This paper proposes use of real superconducting quantum devices as reservoir, where property served by natural noise added bits. The performance this reservoir demonstrated in benchmark time-series regression problem practical classifying different objects based on sensor data. In both cases proposed computer shows...

Classification of molecular structures is a crucial step in dynamics (MD) simulations to detect various and phases within systems. Molecular structures, which are commonly identified using order parameters, were recently machine learning (ML), that is, the ML models acquire structural features labeled crystals or via supervised learning. However, these approaches may not identify unlabeled unknown such as imperfect crystal observed nonequilibrium systems interfaces. In this study, we...

This paper describes an experimental study on the statistical nature of clathrate-hydrate nucleation in a quiescent hydrochlorofluorocarbon-in-water system which hydrate was once formed and then dissociated. The primary objective is to investigate how depends its thermal history (i.e., time evolution temperature), through preceding dissociation carried out, thereby better characterize "memory effect" for formation. Isolated drops HCFC-141b (CH3CCl2F) immersed water were employed as test...

Homogeneous nucleation process in the vapor phase of water is investigated with a molecular dynamics computer simulation at 350 K under supersaturation ratio 7.3. Using method similar to Lennard-Jones fluid (Part I), rate three orders magnitude smaller than prediction classical theory. The kinetically defined critical nucleus size 30–45, much larger thermodynamically value 1.0 estimated Free energy cluster formation from distribution steady state time region. predicted this free agrees...

Structure of cold nuclear matter at subnuclear densities for the proton fraction $x=0.5$, 0.3 and 0.1 is investigated by quantum molecular dynamics (QMD) simulations. We demonstrate that phases with slablike rodlike nuclei, etc. can be formed dynamically from hot uniform without any assumptions on shape, also systematically analyze structure using two-point correlation functions Minkowski functionals. In our simulations, we observe intermediate phases, which has complicated shapes. It found...

Calculations of equilibrium properties dense matter predict that at subnuclear densities nuclei can be rodlike or slablike. To investigate whether transitions between phases with nonspherical occur during the collapse a star, we perform quantum molecular dynamic simulations compression matter. We have succeeded in simulating and slablike cylindrical bubbles. Our results strongly suggest formed inner cores collapsing stars.

In supernova cores, nuclear "pasta" phases such as a triangular lattice of rodlike nuclei and layered structure slablike are considered to exist. However, it is still unclear whether or not they actually formed in collapsing cores. Using ab initio simulations called quantum molecular dynamics, here we solve this problem by demonstrating that from bcc compression. We also find that, the transition process, system undergoes zigzag configuration elongated nuclei, which fusion two original...

As an entry for the 2009 Gordon Bell price/performance prize, we present results of two different hierarchical N-body simulations on a cluster 256 graphics processing units (GPUs). Unlike many previous GPUs that scale as O(N2), method calculates O(N log N) treecode and O(N) fast multipole (FMM) with unprecedented efficiency. We demonstrate performance our by choosing one standard application --a gravitational simulation-- non-standard --simulation turbulence using vortex particles. The...

Anomalous diffusion in lipid bilayers is usually attributed to viscoelastic behavior. We compute the scaling exponent of relative fluctuations time-averaged mean square displacement a bilayer, by using molecular dynamics simulation. According continuous time random walk theory, this indicates non-Gaussian behavior caused power-law trapping time. Our results provide first evidence that bilayer has not only properties but also times distributed according power law.

Kesterite semiconductors, particularly Cu2ZnSnS4 (CZTS), have attracted attention for thin-film solar cells. We investigate the incorporation of Fe into CZTS to form Cu2(Zn,Fe)SnS4 solid-solution tuning lattice spacing and band gap. First-principles calculations confirm a phase transition from kesterite (Zn-rich) stannite (Fe-rich) at Fe/Zn ∼ 0.4. The exothermic enthalpy mixing is consistent with high solubility in lattice. There linear band-gap bowing each phase, which results blue-shift...

Sr₂VFeAsO_3−δ remarkably enhances the oxygen evolution reaction by direct O–O bond formation between OH⁻ coupled oxygen-vacant sites.

Highlights•Interactions of 13 different PH domains with PIP-containing membranes are simulated•PH associate PIPs in via a positively charged loop•Binding causes clustering PIP molecules within membranes•Simulations reveal canonical and alternative binding modes to domainsSummaryA molecular simulation pipeline for determining the mode interaction pleckstrin homology (PH) phosphatidylinositol phosphate (PIP)-containing lipid bilayers is presented. We evaluate our methodology GRP1 domain...

The number of interacting lipids regulates the diffusivity a peripheral membrane protein bound on surface.

Water molecules play an important role in providing unique environments for biological reactions on cell membranes. It is widely believed that water form bridges connect lipid and stabilize Using all-atom molecular dynamics simulations, we show translational rotational diffusion of membrane surfaces exhibit subdiffusion aging. Moreover, provide evidence both divergent mean trapping time (continuous-time random walk) long-correlated noise (fractional Brownian motion) contribute to this...

Clathrate hydrates are solid crystalline structures most commonly formed from solutions that have nucleated to form a mixed composed of water and gas. Understanding the mechanism clathrate hydrate nucleation is essential grasp fundamental chemistry these complex their applications. Molecular dynamics (MD) simulation an ideal method study at molecular level because size critical nucleus formation rate occur on nano scale. Various analysis methods for been developed through MD analyze...

ABSTRACT The spike protein of SARS‐CoV‐2 is a challenging target for theoretical approaches. Here we report benchmark calculation the droplet model by fragment molecular orbital (FMO) at second‐order Møller‐Plesset perturbation (MP2) level on supercomputer Fugaku. One hundred structure samples from dynamics (MD) simulations were used both closed and open forms this (PDB IDs 6XLU 6XM0 respectively). number total fragments about 20,000, job time per was 2 h 8 racks

Protein–RNA condensates are involved in a range of cellular activities. Coarse-grained molecular models intrinsically disordered proteins have been developed to shed light on and predict single-chain properties phase separation. An RNA model compatible with such for would enable the study complex biomolecular mixtures involving RNA. Here, we present sequence-independent coarse-grained, two-beads-per-nucleotide disordered, flexible based hydropathy scale. We parametrize model, which term...

We report large-scale atomistic simulation of midrange nanoscale hydrophobic interaction, manifested by the nucleation nanobubble between nanometer-sized hydrophobes at constrained equilibrium. When length scale is greater than 2 nm, formation shows hysteresis behavior resembling first-order transition. Calculation potential mean force versus interhydrophobe distance provides a quantitative measure strength interaction.

We study self-assembly and polymorphic transitions of surfactant molecules in water within a nanotube the effect water-nanotube interactions on morphologies. present simulation evidence cornucopia structures assemblies--many which have not been observed bulk solutions--through adjusting chemical range from hydrophilic to hydroneutral hydrophobic. The ability control morphologies assemblies nanoscale confinement can be used for patterning interior surface nanochannels application nanofluidics...

We examine the model dependence of phase diagram inhomogeneous nulcear matter in supernova cores using quantum molecular dynamics (QMD). Inhomogeneous includes crystallized with nonspherical nuclei---``pasta'' phases---and liquid-gas phase-separating nuclear matter. Major differences between diagrams QMD models can be explained by energy pure neutron at low densities and saturation density asymmetric show symmetry is also useful to understand uncertainties diagram. point out that, for...