arXiv subjects

Noam Bernstein

Publications and source records attributed to Noam Bernstein.

32 records · Page 2Linked to original sources

arXiv2017

Machine Learning Unifies the Modelling of Materials and Molecules

Determining the stability of molecules and condensed phases is the cornerstone of atomistic modelling, underpinning our understanding of chemical and materials properties and transformations. Here we show that a machine learning model, based on a local description of chemical environments and Bayesian statistical learning, provides a unified framework to predict atomic-scale properties. It captures the quantum mechanical effects governing the complex surface reconstructions of silicon, predicts the stability of different classes of molecules with chemical accuracy, and distinguishes active and inactive protein ligands with more than 99% reliability. The universality and the systematic nature of our framework provides new insight into the potential energy surface of materials and molecules.

cond-mat.mtrl-sci↗

arXiv2017

Constant-pressure nested sampling with atomistic dynamics

The nested sampling algorithm has been shown to be a general method for calculating the pressure-temperature-composition phase diagrams of materials. While the previous implementation used single-particle Monte Carlo moves, these are inefficient for condensed systems with general interactions where single-particle moves cannot be evaluated faster than the energy of the whole system. Here we enhance the method by using all-particle moves: either Galilean Monte Carlo or a total enthalpy Hamiltonian Monte Carlo algorithm, introduced in this paper. We show that these algorithms enable the determination of phase transition temperatures with equivalent accuracy to the previous method at $1/N$ of the cost for an $N$-particle system with general interactions, or at equal cost when single particle moves can be done in $1/N$ of the cost of a full $N$-particle energy evaluation.

cond-mat.stat-mech↗

arXiv2017

Bright triplet excitons in lead halide perovskites

Nanostructured semiconductors emit light from electronic states known as excitons[1]. According to Hund's rules[2], the lowest energy exciton in organic materials should be a poorly emitting triplet state. Analogously, the lowest exciton level in all known inorganic semiconductors is believed to be optically inactive. These 'dark' excitons (into which the system can relax) hinder light-emitting devices based on semiconductor nanostructures. While strategies to diminish their influence have been developed[3-5], no materials have been identified in which the lowest exciton is bright. Here we show that the lowest exciton in quasi-cubic lead halide perovskites is optically active. We first use the effective-mass model and group theory to explore this possibility, which can occur when the strong spin-orbit coupling in the perovskite conduction band is combined with the Rashba effect [6-10]. We then apply our model to CsPbX3 (X=Cl,Br,I) nanocrystals[11], for which we measure size- and composition-dependent fluorescence at the single-nanocrystal level. The bright character of the lowest exciton immediately explains the anomalous photon-emission rates of these materials, which emit 20 and 1,000 times faster[12] than any other semiconductor nanocrystal at room[13-16] and cryogenic[17] temperatures, respectively. The bright exciton is further confirmed by detailed analysis of the fine structure in low-temperature fluorescence spectra. For semiconductor nanocrystals[18], which are already used in lighting[19,20], lasers[21,22], and displays[23], these optically active excitons can lead to materials with brighter emission and enhanced absorption. More generally, our results provide criteria for identifying other semiconductors exhibiting bright excitons with potentially broad implications for optoelectronic devices.

cond-mat.mes-hall↗

arXiv2016

Modulus-Pressure Equation for Confined Fluids

Ultrasonic experiments allow one to measure the elastic modulus of bulk solid or fluid samples. Recently such experiments have been carried out on fluid-saturated nanoporous glass to probe the modulus of a confined fluid. In our previous work [J. Chem. Phys., (2015) 143, 194506], using Monte Carlo simulations we showed that the elastic modulus $K$ of a fluid confined in a mesopore is a function of the pore size. Here we focus on modulus-pressure dependence $K(P)$, which is linear for bulk materials, a relation known as the Tait-Murnaghan equation. Using transition-matrix Monte Carlo simulations we calculated the elastic modulus of bulk argon as a function of pressure and argon confined in silica mesopores as a function of Laplace pressure. Our calculations show that while the elastic modulus is strongly affected by confinement and temperature, the slope of the modulus versus pressure is not. Moreover, the calculated slope is in a good agreement with the reference data for bulk argon and experimental data for confined argon derived from ultrasonic experiments. We propose to use the value of the slope of $K(P)$ to estimate the elastic moduli of an unknown porous medium.

physics.chem-ph↗

arXiv2016

A universal preconditioner for simulating condensed phase materials

We introduce a universal sparse preconditioner that accelerates geometry optimisation and saddle point search tasks that are common in the atomic scale simulation of materials. Our preconditioner is based on the neighbourhood structure and we demonstrate the gain in computational efficiency in a wide range of materials that include metals, insulators and molecular solids. The simple structure of the preconditioner means that the gains can be realised in practice not only when using expensive electronic structure models but also for fast empirical potentials. Even for relatively small systems of a few hundred atoms, we observe speedups of a factor of two or more, and the gain grows with system size. An open source Python implementation within the Atomic Simulation Environment is available, offering interfaces to a wide range of atomistic codes.

cond-mat.mtrl-sci↗

arXiv2015

Relation Between Pore Size and the Compressibility of a Confined Fluid

When a fluid is confined to a nanopore, its thermodynamic properties differ from the properties of a bulk fluid, so measuring such properties of the confined fluid can provide information about the pore sizes. Here we report a simple relation between the pore size and isothermal compressibility of argon confined in these pores. Compressibility is calculated from the fluctuations of the number of particles in the grand canonical ensemble using two different simulation techniques: conventional grand-canonical Monte Carlo and grand-canonical ensemble transition-matrix Monte Carlo. Our results provide a theoretical framework for extracting the information on the pore sizes of fluid-saturated samples by measuring the compressibility from ultrasonic experiments.

physics.chem-ph↗

arXiv2015

Elastic Response of Mesoporous Silicon to Capillary Pressures in the Pores

We study water adsorption-induced deformation of a monolithic, mesoporous silicon membrane traversed by independent channels of $\sim$8 nm diameter. We focus on the elastic constant associated with the Laplace pressure-induced deformation of the membrane upon capillary condensation, i.e. the pore-load modulus. We perform finite-element method (FEM) simulations of the adsorption-induced deformation of hexagonal and square lattices of cylindrical pores representing the membrane. We find that the pore-load modulus weakly depends on the geometrical arrangement of pores, and can be expressed as a function of porosity. We propose an analytical model which relates the pore-load modulus to the porosity and to the elastic properties of bulk silicon (Young's modulus and Poisson's ratio), and provides an excellent agreement with FEM results. We find good agreement between our experimental data and the predictions of the analytical model, with the Young's modulus of the pore walls slightly lower than the bulk value. This model is applicable to a large class of materials with morphologies similar to mesoporous silicon. Moreover, our findings suggest that liquid condensation experiments allow one to elegantly access the elastic constants of a mesoporous medium.

cond-mat.mes-hall↗

arXiv2014

The Adaptive Buffered Force QM/MM method in the CP2K and AMBER software packages

The implementation and validation of the adaptive buffered force QM/MM method in two popular packages, CP2K and AMBER are presented. The implementations build on the existing QM/MM functionality in each code, extending it to allow for redefinition of the QM and MM regions during the simulation and reducing QM-MM interface errors by discarding forces near the boundary according to the buffered force-mixing approach. New adaptive thermostats, needed by force-mixing methods, are also implemented. Different variants of the method are benchmarked by simulating the structure of bulk water, water autoprotolysis in the presence of zinc and dimethyl-phosphate hydrolysis using various semiempirical Hamiltonians and density functional theory as the QM model. It is shown that with suitable parameters, based on force convergence tests, the adaptive buffered-force QM/MM scheme can provide an accurate approximation of the structure in the dynamical QM region matching the corresponding fully QM simulations, as well as reproducing the correct energetics in all cases. Adaptive unbuffered force-mixing and adaptive conventional QM/MM methods also provide reasonable results for some systems, but are more likely to suffer from instabilities and inaccuracies.

physics.chem-ph↗

arXiv2014

Free energy surface reconstruction from umbrella samples using Gaussian process regression II: Multiple collective variables

We demonstrate how a prior assumption of smoothness can be used to enhance the reconstruction of free energy profiles from multiple umbrella sampling simulations using the Bayesian Gaussian process regression approach. The method we derive allows the concurrent use of histograms and free energy gradients and can easily be extended to include further data. In Part I we review the necessary theory and test the method for one collective variable. We demonstrate improved performance with respect to the weighted histogram analysis method and obtain meaningful error bars without any significant additional computation. In Part II we consider the case of multiple collective variables and compare to a reconstruction using least squares fitting of radial basis functions. We find substantial improvements in the regimes of spatially sparse data or short sampling trajectories. A software implementation is made available on www.libatoms.org.

cond-mat.stat-mech↗

arXiv2014

Free energy surface reconstruction from umbrella samples using Gaussian process regression

We demonstrate how the Gaussian process regression approach can be used to efficiently reconstruct free energy surfaces from umbrella sampling simulations. By making a prior assumption of smoothness and taking account of the sampling noise in a consistent fashion, we achieve a significant improvement in accuracy over the state of the art in two or more dimensions or, equivalently, a significant cost reduction to obtain the free energy surface within a prescribed tolerance in both regimes of spatially sparse data and short sampling trajectories. Stemming from its Bayesian interpretation the method provides meaningful error bars without significant additional computation. A software implementation is made available on www.libatoms.org.

cond-mat.stat-mech↗

arXiv2004

Incommensurate Transverse Anisotropy Induced by Disorder and Spin-Orbit-Vibron Coupling in Mn12-acetate

It has been shown within density-functional theory that in Mn$_{12}$-acetate there are effects due to disorder by solvent molecules and a coupling between vibrational and electronic degrees of freedom. We calculate the in-plane principal axes of the second-order anisotropy caused by the second effect and compare them with those of the fourth-order anisotropy due to the first effect. We find that the two types of the principal axes are not commensurate with each other, which results in a complete quenching of the tunnel-splitting oscillation as a function of an applied transverse field.

cond-mat.mtrl-sci↗

arXiv2003

Second-order transverse magnetic anisotropy induced by disorders in the single-molecule magnet Mn12

For the single-molecule magnet Mn12, Cornia et al. recently proposed that solvent molecules may cause the quantum tunneling that requires a lower symmetry than S4. However, magnetic quantum tunneling and electron paramagnetic resonance experiments suggested that the proposed theory may not correspond to the measurements. In this regard, we consider positional disorder induced by the solvent molecules and orientational disorder by the methyl groups of a Mn12 molecule. We calculate, within density-functional theory, the second-order transverse magnetic anisotropy parameter E and an easy-axis tilting angle induced by the positional disorder and the E value by the orientational disorder. We also calculate the local magnetic anisotropy and the local easy axis for each inequivalent Mn site in different environments to investigate their effects on the global E value. We find that the hydrogen bonding between a Mn12 molecule and the solvent molecule is crucial to obtain a substantial E value and that the E value increases upon geometry relaxations. Our calculations on relaxed geometries show that the largest calculated E value is 0.016 K and that the largest tilting angle is 0.5 degrees. Our largest E value is comparable to experimental results but larger than Cornia et al.'s.

cond-mat.mtrl-sci↗

arXiv2003

Electronic, magnetic, and vibrational properties of the molecular magnet Mn4 monomer and dimer

A new type of the single-molecule magnet [Mn_4 O_3 Cl_4 (O_2 CEt)_3(py)_3] forms dimers. Recent magnetic hysteresis measurements on this single-molecular magnet revealed interesting phenomena: an absence of quantum tunneling at zero magnetic field and tunneling before magnetic field reversal. This is attributed to a significant antiferromagnetic exchange interaction between different monomers. To investigate this system, we calculate the electronic structure, magnetic properties, intramolecular and intermolecular exchange interactions using density-functional theory within the generalized-gradient approximation. Our calculations agree with experiment. We also calculate vibrational infrared absorption and Raman scattering intensities for the monomer which can be tested experimentally.

cond-mat.mtrl-sci↗

arXiv2002

Vibrationally induced fourth-order magnetic anisotropy and tunnel splittings in Mn_{12}

From density-functional-theory (DFT) based methods we calculate the vibrational spectrum of the Mn_{12}O_{12}(COOH)_{16}(H_2 O)_4 molecular magnet. Calculated infrared intensities are in accord with experimental studies. There have been no ab initio attempts at determining which interactions account for the fourth-order anisotropy. We show that vibrationally induced distortions of the molecule contribute to the fourth-order anisotropy Hamiltonian and that the magnitude and sign of the effect (-6.2 K) is in good agreement with all experiments. Vibrationally induced tunnel splittings in isotopically pure and natural samples are predicted.

cond-mat.mtrl-sci↗