Martinsenglenn0319

The persistent problem posed by the glass transition is to develop a general atomic level description of amorphous solidification. The answer proposed in this paper is to measure a configuration's capacity to restrain the motion of the constituent atoms. Here, we show that the instantaneous normal modes can be used to define a measure of atomic restraint that accounts for the difference between fragile and strong liquids and the collective length scale of the supercooled liquid. These results represent a significant simplification of the description of amorphous solidification and provide a powerful systematic treatment of the influence of microscopic factors on the formation of an amorphous solid.The convergence of the recently developed cluster perturbation (CP) expansions [Pawlowski et al., J. Chem. Phys. 150, 134108 (2019)] is analyzed with the double purpose of developing the mathematical tools and concepts needed to describe these expansions at general order and to identify the factors that define the rate of convergence of CP series. To this end, the CP energy, amplitude, and Lagrangian multiplier equations as a function of the perturbation strength are developed. Selleck SR-4835 By determining the critical points, defined as the perturbation strengths for which the Jacobian becomes singular, the rate of convergence and the intruder and critical states are determined for five small molecules BH, CO, H2O, NH3, and HF. To describe the patterns of convergence for these expansions at orders lower than the high-order asymptotic limit, a model is developed where the perturbation corrections arise from two critical points. It is shown that this model allows for rationalization of the behavior of the perturbation corrections at much lower order than required for the onset of the asymptotic convergence. For the H2O, CO, and HF molecules, the pattern and rate of convergence are defined by critical states where the Fock-operator underestimates the excitation energies, whereas the pattern and rate of convergence for BH are defined by critical states where the Fock-operator overestimates the excitation energy. For the NH3 molecule, both forms of critical points are required to describe the convergence behavior up to at least order 25.Photosynthetic light-harvesting complexes have a remarkable capacity to perform robust photo-physics at ambient temperatures and in fluctuating environments. Protein conformational dynamics and membrane mobility are processes that contribute to the light-harvesting efficiencies and control photoprotective responses. This short review describes the application of magic angle spinning nuclear magnetic resonance (NMR) spectroscopy for characterizing the structural dynamics of pigment, protein, and thylakoid membrane components related to light harvesting and photoprotection. I will discuss the use of dynamics-based spectral editing solid-state NMR for distinguishing rigid and mobile components and assessing protein, pigment, and lipid dynamics on sub-nanosecond to millisecond timescales. Dynamic spectral editing NMR has been applied to investigate light-harvesting complex II protein conformational dynamics inside lipid bilayers and in native membranes. Furthermore, we used the NMR approach to assess thylakoid membrane dynamics. Finally, it is shown that dynamics-based spectral editing NMR for reducing spectral complexity by filtering motion-dependent signals enabled us to follow processes in live photosynthetic cells.Equilibrium structures determine material properties and biochemical functions. We here propose to machine learn phase space averages, conventionally obtained by ab initio or force-field-based molecular dynamics (MD) or Monte Carlo (MC) simulations. In analogy to ab initio MD, our ab initio machine learning (AIML) model does not require bond topologies and, therefore, enables a general machine learning pathway to obtain ensemble properties throughout the chemical compound space. We demonstrate AIML for predicting Boltzmann averaged structures after training on hundreds of MD trajectories. The AIML output is subsequently used to train machine learning models of free energies of solvation using experimental data and to reach competitive prediction errors (mean absolute error ∼ 0.8 kcal/mol) for out-of-sample molecules-within milliseconds. As such, AIML effectively bypasses the need for MD or MC-based phase space sampling, enabling exploration campaigns of Boltzmann averages throughout the chemical compound space at a much accelerated pace. We contextualize our findings by comparison to state-of-the-art methods resulting in a Pareto plot for the free energy of solvation predictions in terms of accuracy and time.The chemical model of matter consists of atoms held together by bonds. The success of this model implies that the physical interactions of the electrons and nuclei in molecules combine into compound interactions that create the bonding. In the quantum mechanical description, the modified atoms in molecules and the bonding synergism are contained in the molecular electronic wave function. So far, only part of this information has been recovered from the wave function. Notably, the atoms have remained unidentified in the wave function. One reason is that conventional energy decomposition analyses formulate separate model wave functions, independent of the actual wave function, to represent "prepared atoms" and preconceived interactions and, then, intuitively catenate the parts. In the present work, the embedded modified atoms and the inherent physical synergisms between them are determined by a unified derivation entirely from the actual molecular valence space wave function. By means of a series of intrinsic orbital and configurational transformations of the wave function, the energy of formation of a molecule is additively resolved in terms of intra-atomic energy changes, interference energies, and quasi-classical, non-classical, and charge-transfer Coulombic interactions. The analysis furnishes an algorithm for the quantitative resolution of the energy of formation, which enables analyses elucidating reaction energies.We present a classical induction model to evaluate the three-body ion-water-water (I-W-W) and water-water-water (W-W-W) interactions in aqueous ionic systems. The classical description of the induction energy is based on electrostatic distributed multipoles up to hexadecapole and distributed polarizabilities up to quadrupole-quadrupole on the O and H atoms of water. The monatomic ions were described by a point charge and a dipole-dipole polarizability, while for the polyatomic ions, distributed multipoles up to hexadecapole and distributed polarizabilities up to quadrupole-quadrupole were used. The accuracy of the classical model is benchmarked against an accurate dataset of 936 (I-W-W) and 2184 (W-W-W) three-body terms for 13 different monatomic and polyatomic cation and anion systems. The classical model shows excellent agreement with the reference second order Moller-Plesset and coupled-cluster single double and perturbative triple [CCSD(T)] three-body energies. The Root-Mean-Square-Errors (RMSEs) for monatomic cations, monatomic anions, and polyatomic ions were 0.29, 0.25, and 0.12 kcal/mol, respectively. The corresponding RMSE for 1744 CCSD(T)/aVTZ three-body (W-W-W) energies, used to train MB-pol, was 0.12 kcal/mol. The accuracy of the proposed classical model demonstrates that the three-body term for aqueous ionic systems can be accurately modeled classically. This approach provides a fast, efficient, and as-accurate path toward modeling the three-body term in aqueous ionic systems that is fully transferable across systems with different ions without the need to fit to tens of thousands of ab initio calculations for each ion to extend existing many-body force fields to interactions between water and ions.Despite its simple molecular formula, obtaining an accurate in silico description of water is far from straightforward. Many of its very peculiar properties are quite elusive, and in particular, obtaining good estimations of the diffusion coefficients of the solvated proton and hydroxide at a reasonable computational cost has been an unsolved challenge until now. Here, I present extensive results of several unusually long ab initio molecular dynamics (MD) simulations employing different combinations of the Born-Oppenheimer and second-generation Car-Parrinello MD propagation methods with different ensembles (NVE and NVT) and thermostats, which show that these methods together with the RPBE-D3 functional provide a very accurate estimation of the diffusion coefficients of the solvated H3O+ and OH- ions, together with an extremely accurate description of several properties of neutral water (such as the structure of the liquid and its diffusion and shear viscosity coefficients). In addition, I show that the estimations of DH3O+ and DOH- depend dramatically on the simulation length, being necessary to reach timescales in the order of hundreds of picoseconds to obtain reliable results.Spherically symmetric atom-centered descriptors of atomic environments have been widely used for constructing potential or free energy surfaces of atomistic and colloidal systems and to characterize local structures using machine learning techniques. However, when particle shapes are non-spherical, as in the case of rods and ellipsoids, standard spherically symmetric structure functions alone produce imprecise descriptions of local environments. In order to account for the effects of orientation, we introduce two- and three-body orientation-dependent particle-centered descriptors for systems composed of rod-like particles. To demonstrate the suitability of the proposed functions, we use an efficient feature selection scheme and simple linear regression to construct coarse-grained many-body interaction potentials for computationally efficient simulations of model systems consisting of colloidal particles with an anisotropic shape mixtures of colloidal rods and non-adsorbing polymer coils, hard rods enclosed by an elastic microgel shell, and ligand-stabilized nanorods. We validate the machine-learning (ML) effective many-body potentials based on orientation-dependent symmetry functions by using them in direct coexistence simulations to map out the phase behavior of colloidal rods and non-adsorbing polymer coils. We find good agreement with the results obtained from simulations of the true binary mixture, demonstrating that the effective interactions are well described by the orientation-dependent ML potentials.We have extended cluster perturbation (CP) theory to comprehend the calculation of first order properties (FOPs). We have determined CP FOP series where FOPs are determined as a first energy derivative and also where the FOPs are determined as a generalized expectation value of the external perturbation operator over the coupled cluster state and its biorthonormal multiplier state. For S(D) orbital excitation spaces, we find that the CP series for FOPs that are determined as a first derivative, in general, in second order have errors of a few percent in the singles and doubles correlation contribution relative to the targeted coupled cluster (CC) results. For a SD(T) orbital excitation space, we find that the CP series for FOPs determined as a generalized expectation value in second order have errors of about ten percent in the triples correlation contribution relative to the targeted CC results. These second order models, therefore, constitute viable alternatives for determining high quality FOPs.