Surveying the energy landscape of coarse-grained mappings.

Simulations of soft materials often adopt low-resolution coarse-grained (CG) models. However, the CG representation is not unique and its impact upon simulated properties is poorly understood. In this work, we investigate the space of CG representations for ubiquitin, which is a typical globular protein with 72 amino acids. We employ Monte Carlo methods to ergodically sample this space and to characterize its landscape. By adopting the Gaussian network model as an analytically tractable atomistic model for equilibrium fluctuations, we exactly assess the intrinsic quality of each CG representation without introducing any approximations in sampling configurations or in modeling interactions. We focus on two metrics, the spectral quality and the information content, that quantify the extent to which the CG representation preserves low-frequency, large-amplitude motions and configurational information, respectively. The spectral quality and information content are weakly correlated among high-resolution representations but become strongly anticorrelated among low-resolution representations. Representations with maximal spectral quality appear consistent with physical intuition, while low-resolution representations with maximal information content do not. Interestingly, quenching studies indicate that the energy landscape of mapping space is very smooth and highly connected. Moreover, our study suggests a critical resolution below which a "phase transition" qualitatively distinguishes good and bad representations.

Exploring the landscape of model representations.

The success of any physical model critically depends upon adopting an appropriate representation for the phenomenon of interest. Unfortunately, it remains generally challenging to identify the essential degrees of freedom or, equivalently, the proper order parameters for describing complex phenomena. Here we develop a statistical physics framework for exploring and quantitatively characterizing the space of order parameters for representing physical systems. Specifically, we examine the space of low-resolution representations that correspond to particle-based coarse-grained (CG) models for a simple microscopic model of protein fluctuations. We employ Monte Carlo (MC) methods to sample this space and determine the density of states for CG representations as a function of their ability to preserve the configurational information, I, and large-scale fluctuations, Q, of the microscopic model. These two metrics are uncorrelated in high-resolution representations but become anticorrelated at lower resolutions. Moreover, our MC simulations suggest an emergent length scale for coarse-graining proteins, as well as a qualitative distinction between good and bad representations of proteins. Finally, we relate our work to recent approaches for clustering graphs and detecting communities in networks.

Calculation of Chemical Reaction Barrier Heights by Multiconfiguration Pair-Density Functional Theory with Correlated Participating Orbitals.

The accurate description of reaction barrier heights is challenging for quantum mechanical methods due to the need for a balanced treatment of dynamic and static correlation energies because their importance varies during the course of a chemical reaction. While some regions of potential energy surfaces are well-described by a single-reference wave function or by Kohn-Sham density functional theory, in other cases a multireference treatment is needed. For systems with many active electrons, most accurate multireference methods have prohibitive computational scalings with system size. Multiconfiguration pair-density functional theory, MC-PDFT, is a more affordable multireference approach that computes the total electron correlation energy in a single step by using the multiconfiguration kinetic energy, density, and on-top pair density and an on-top density functional. In this work, we apply MC-PDFT to a benchmark database (DBH24/18) of 24 diverse reaction barrier heights. We explore the role of active space and basis set selection on the performance of MC-PDFT. We find that MC-PDFT is able to calculate reaction barrier heights with a similar accuracy to complete active space second order perturbation theory, CASPT2, but at a lower computational cost, and we find that MC-PDFT is less dependent on basis set selection than CASPT2.

Analytic Gradients for Complete Active Space Pair-Density Functional Theory.

Analytic gradient routines are a desirable feature for quantum mechanical methods, allowing for efficient determination of equilibrium and transition state structures and several other molecular properties. In this work, we present analytical gradients for multiconfiguration pair-density functional theory (MC-PDFT) when used with a state-specific complete active space self-consistent field reference wave function. Our approach constructs a Lagrangian that is variational in all wave function parameters. We find that MC-PDFT locates equilibrium geometries for several small- to medium-sized organic molecules that are similar to those located by complete active space second-order perturbation theory but that are obtained with decreased computational cost.