Compatible observable decompositions for coarse-grained representations of real molecular systems

Understanding dynamics in coarse-grained models. IV. Connection of fine-grained and coarse-grained dynamics with the Stokes-Einstein and Stokes-Einstein-Debye relations

Applying an excess entropy scaling formalism to the coarse-grained (CG) dynamics of liquids, we discovered that missing rotational motions during the CG process are responsible for artificially accelerated CG dynamics. In the context of the dynamic representability between the fine-grained (FG) and CG dynamics, this work introduces the well-known Stokes-Einstein and Stokes-Einstein-Debye relations to unravel the rotational dynamics underlying FG trajectories, thereby allowing for an indirect evaluation of the effective rotations based only on the translational information at the reduced CG resolution. Since the representability issue in CG modeling limits a direct evaluation of the shear stress appearing in the Stokes-Einstein and Stokes-Einstein-Debye relations, we introduce a translational relaxation time as a proxy to employ these relations, and we demonstrate that these relations hold for the ambient conditions studied in our series of work. Additional theoretical links to our previous work are also established. First, we demonstrate that the effective hard sphere radius determined by the classical perturbation theory can approximate the complex hydrodynamic radius value reasonably well. Furthermore, we present a simple derivation of an excess entropy scaling relationship for viscosity by estimating the elliptical integral of molecules. In turn, since the translational and rotational motions at the FG level are correlated to each other, we conclude that the "entropy-free" CG diffusion only depends on the shape of the reference molecule. Our results and analyses impart an alternative way of recovering the FG diffusion from the CG description by coupling the translational and rotational motions at the hydrodynamic level.

Rigorous Progress in Coarse-Graining

Low-resolution coarse-grained (CG) models provide remarkable computational and conceptual advantages for simulating soft materials. In principle, bottom-up CG models can reproduce all structural and thermodynamic properties of atomically detailed models that can be observed at the resolution of the CG model. This review discusses recent progress in developing theory and computational methods for achieving this promise. We first briefly review variational approaches for parameterizing interaction potentials and their relationship to machine learning methods. We then discuss recent approaches for simultaneously improving both the transferability and thermodynamic properties of bottom-up models by rigorously addressing the density and temperature dependence of these potentials. We also briefly discuss exciting progress in modeling high-resolution observables with low-resolution CG models. More generally, we highlight the essential role of the bottom-up framework not only for fundamentally understanding the limitations of prior CG models but also for developing robust computational methods that resolve these limitations in practice.

Hierarchical Framework for Predicting Entropies in Bottom-Up Coarse-Grained Models

The thermodynamic entropy of coarse-grained (CG) models stands as one of the most important properties for quantifying the missing information during the CG process and for establishing transferable (or extendible) CG interactions. However, performing additional CG simulations on top of model construction often leads to significant additional computational overhead. In this work, we propose a simple hierarchical framework for predicting the thermodynamic entropies of various molecular CG systems. Our approach employs a decomposition of the CG interactions, enabling the estimation of the CG partition function and thermodynamic properties a priori. Starting from the ideal gas description, we leverage classical perturbation theory to systematically incorporate simple yet essential interactions, ranging from the hard sphere model to the generalized van der Waals model. Additionally, we propose an alternative approach based on multiparticle correlation functions, allowing for systematic improvements through higher-order correlations. Numerical applications to molecular liquids validate the high fidelity of our approach, and our computational protocols demonstrate that a reduced model with simple energetics can reasonably estimate the thermodynamic entropy of CG models without performing any CG simulations. Overall, our findings present a systematic framework for estimating not only the entropy but also other thermodynamic properties of CG models, relying solely on information from the reference system.

Structural Coarse-Graining via Multiobjective Optimization with Differentiable Simulation

In the realm of multiscale molecular simulations, structure-based coarse-graining is a prominent approach for creating efficient coarse-grained (CG) representations of soft matter systems, such as polymers. This involves optimizing CG interactions by matching static correlation functions of the corresponding degrees of freedom in all-atom (AA) models. Here, we present a versatile method, namely, differentiable coarse-graining (DiffCG), which combines multiobjective optimization and differentiable simulation. The DiffCG approach is capable of constructing robust CG models by iteratively optimizing the effective potentials to simultaneously match multiple target properties. We demonstrate our approach by concurrently optimizing bonded and nonbonded potentials of a CG model of polystyrene (PS) melts. The resulting CG-PS model effectively reproduces both the structural characteristics, such as the equilibrium probability distribution of microscopic degrees of freedom and the thermodynamic pressure of the AA counterpart. More importantly, leveraging the multiobjective optimization capability, we develop a precise and efficient CG model for PS melts that is transferable across a wide range of temperatures, i.e., from 400 to 600 K. It is achieved via optimizing a pairwise potential with nonlinear temperature dependence in the CG model to simultaneously match target data from AA-MD simulations at multiple thermodynamic states. The temperature transferable CG-PS model demonstrates its ability to accurately predict the radial distribution functions and density at different temperatures, including those that are not included in the target thermodynamic states. Our work opens up a promising route for developing accurate and transferable CG models of complex soft-matter systems through multiobjective optimization with differentiable simulation.

Perturbative Expansion in Reciprocal Space: Bridging Microscopic and Mesoscopic Descriptions of Molecular Interactions

Determining the Fourier representation of various molecular interactions is important for constructing density-based field theories from a microscopic point of view, enabling a multiscale bridge between microscopic and mesoscopic descriptions. However, due to the strongly repulsive nature of short-ranged interactions, interparticle interactions cannot be formally defined in Fourier space, which renders coarse-grained (CG) approaches in k-space somewhat ambiguous. In this paper, we address this issue by designing a perturbative expansion of pair interactions in reciprocal space. Our perturbation theory, starting from reciprocal space, elucidates the microscopic origins underlying zeroth-order (long-range attractions) and divergent repulsive interactions from higher order contributions. We propose a systematic framework for constructing a faithful Fourier-space representation of molecular interactions, capturing key structural correlations in various systems, including simple model systems and molecular CG models of liquids. Building upon the Ornstein-Zernike equation, our approach can be combined with appropriate closure relations, and to further improve the closure approximations, we develop a bottom-up parameterization strategy for inferring the bridge function from microscopic statistics. By incorporating the bridge function into the Fourier representation, our findings suggest a systematic, bottom-up approach to performing coarse-graining in reciprocal space, leading to the systematic construction of a bottom-up classical field theory of complex aqueous systems.

Gaussian representation of coarse-grained interactions of liquids: Theory, parametrization, and transferability

Coarse-grained (CG) interactions determined via bottom-up methodologies can faithfully reproduce the structural correlations observed in fine-grained (atomistic resolution) systems, yet they can suffer from limited extensibility due to complex many-body correlations. As part of an ongoing effort to understand and improve the applicability of bottom-up CG models, we propose an alternative approach to address both accuracy and transferability. Our main idea draws from classical perturbation theory to partition the hard sphere repulsive term from effective CG interactions. We then introduce Gaussian basis functions corresponding to the system's characteristic length by linking these Gaussian sub-interactions to the local particle densities at each coordination shell. The remaining perturbative long-range interaction can be treated as a collective solvation interaction, which we show exhibits a Gaussian form derived from integral equation theories. By applying this numerical parametrization protocol to CG liquid systems, our microscopic theory elucidates the emergence of Gaussian interactions in common phenomenological CG models. To facilitate transferability for these reduced descriptions, we further infer equations of state to determine the sub-interaction parameter as a function of the system variables. The reduced models exhibit excellent transferability across the thermodynamic state points. Furthermore, we propose a new strategy to design the cross-interactions between distinct CG sites in liquid mixtures. This involves combining each Gaussian in the proper radial domain, yielding accurate CG potentials of mean force and structural correlations for multi-component systems. Overall, our findings establish a solid foundation for constructing transferable bottom-up CG models of liquids with enhanced extensibility.

Utilizing Machine Learning to Greatly Expand the Range and Accuracy of Bottom-Up Coarse-Grained Models through Virtual Particles

Coarse-grained (CG) models parametrized using atomistic reference data, i.e., "bottom up" CG models, have proven useful in the study of biomolecules and other soft matter. However, the construction of highly accurate, low resolution CG models of biomolecules remains challenging. We demonstrate in this work how virtual particles, CG sites with no atomistic correspondence, can be incorporated into CG models within the context of relative entropy minimization (REM) as latent variables. The methodology presented, variational derivative relative entropy minimization (VD-REM), enables optimization of virtual particle interactions through a gradient descent algorithm aided by machine learning. We apply this methodology to the challenging case of a solvent-free CG model of a 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC) lipid bilayer and demonstrate that introduction of virtual particles captures solvent-mediated behavior and higher-order correlations which REM alone cannot capture in a more standard CG model based only on the mapping of collections of atoms to the CG sites.

Flow-Matching: Efficient Coarse-Graining of Molecular Dynamics without Forces

Coarse-grained (CG) molecular simulations have become a standard tool to study molecular processes on time and length scales inaccessible to all-atom simulations. Parametrizing CG force fields to match all-atom simulations has mainly relied on force-matching or relative entropy minimization, which require many samples from costly simulations with all-atom or CG resolutions, respectively. Here we present flow-matching, a new training method for CG force fields that combines the advantages of both methods by leveraging normalizing flows, a generative deep learning method. Flow-matching first trains a normalizing flow to represent the CG probability density, which is equivalent to minimizing the relative entropy without requiring iterative CG simulations. Subsequently, the flow generates samples and forces according to the learned distribution in order to train the desired CG free energy model via force-matching. Even without requiring forces from the all-atom simulations, flow-matching outperforms classical force-matching by an order of magnitude in terms of data efficiency and produces CG models that can capture the folding and unfolding transitions of small proteins.

Enhancing pressure consistency and transferability of structure-based coarse-graining

Coarse-graining, which models molecules with coarse-grained (CG) beads, allows molecular dynamics simulations to be applied to systems with large length and time scales while preserving the essential molecular structure. However, CG models generally have insufficient representability and transferability. A commonly used method to resolve this problem is multi-state iterative Boltzmann inversion (MS-IBI) with pressure correction, which matches both the structural properties and pressures at different thermodynamic states between CG and all-atom (AA) simulations. Nevertheless, this method is usually effective only in a narrow pressure range. In this paper, we propose a modified CG scheme to overcome this limitation. We find that the fundamental reason for this limitation is that CG beads at close distances are ellipsoids rather than isotropically compressed spheres, as described in conventional CG models. Hence, we propose a method to compensate for such differences by slightly modifying the radial distribution functions (RDFs) derived from AA simulations and using the modified RDFs as references for pressure-corrected MS-IBI. We also propose a method to determine the initial non-bonded potential using both the target RDF and pressure. Using n-dodecane as a case study, we demonstrate that the CG model developed using our scheme reproduces the RDFs and pressures over a wide range of pressure states, including three reference low-pressure states and two test high-pressure states. The proposed scheme allows for accurate CG simulations of systems in which pressure or density varies with time and/or position.

Bottom-up Coarse-Graining: Principles and Perspectives

Large-scale computational molecular models provide scientists a means to investigate the effect of microscopic details on emergent mesoscopic behavior. Elucidating the relationship between variations on the molecular scale and macroscopic observable properties facilitates an understanding of the molecular interactions driving the properties of real world materials and complex systems (e.g., those found in biology, chemistry, and materials science). As a result, discovering an explicit, systematic connection between microscopic nature and emergent mesoscopic behavior is a fundamental goal for this type of investigation. The molecular forces critical to driving the behavior of complex heterogeneous systems are often unclear. More problematically, simulations of representative model systems are often prohibitively expensive from both spatial and temporal perspectives, impeding straightforward investigations over possible hypotheses characterizing molecular behavior. While the reduction in resolution of a study, such as moving from an atomistic simulation to that of the resolution of large coarse-grained (CG) groups of atoms, can partially ameliorate the cost of individual simulations, the relationship between the proposed microscopic details and this intermediate resolution is nontrivial and presents new obstacles to study. Small portions of these complex systems can be realistically simulated. Alone, these smaller simulations likely do not provide insight into collectively emergent behavior. However, by proposing that the driving forces in both smaller and larger systems (containing many related copies of the smaller system) have an explicit connection, systematic bottom-up CG techniques can be used to transfer CG hypotheses discovered using a smaller scale system to a larger system of primary interest. The proposed connection between different CG systems is prescribed by (i) the CG representation (mapping) and (ii) the functional form and parameters used to represent the CG energetics, which approximate potentials of mean force (PMFs). As a result, the design of CG methods that facilitate a variety of physically relevant representations, approximations, and force fields is critical to moving the frontier of systematic CG forward. Crucially, the proposed connection between the system used for parametrization and the system of interest is orthogonal to the optimization used to approximate the potential of mean force present in all systematic CG methods. The empirical efficacy of machine learning techniques on a variety of tasks provides strong motivation to consider these approaches for approximating the PMF and analyzing these approximations.

From System Modeling to System Analysis: The Impact of Resolution Level and Resolution Distribution in the Computer-Aided Investigation of Biomolecules

The ever increasing computer power, together with the improved accuracy of atomistic force fields, enables researchers to investigate biological systems at the molecular level with remarkable detail. However, the relevant length and time scales of many processes of interest are still hardly within reach even for state-of-the-art hardware, thus leaving important questions often unanswered. The computer-aided investigation of many biological physics problems thus largely benefits from the usage of coarse-grained models, that is, simplified representations of a molecule at a level of resolution that is lower than atomistic. A plethora of coarse-grained models have been developed, which differ most notably in their granularity; this latter aspect determines one of the crucial open issues in the field, i.e. the identification of an optimal degree of coarsening, which enables the greatest simplification at the expenses of the smallest information loss. In this review, we present the problem of coarse-grained modeling in biophysics from the viewpoint of system representation and information content. In particular, we discuss two distinct yet complementary aspects of protein modeling: on the one hand, the relationship between the resolution of a model and its capacity of accurately reproducing the properties of interest; on the other hand, the possibility of employing a lower resolution description of a detailed model to extract simple, useful, and intelligible information from the latter.

Investigating the energetic and entropic components of effective potentials across a glass transition

By eliminating unnecessary details, coarse-grained (CG) models provide the necessary efficiency for simulating scales that are inaccessible to higher resolution models. However, because they average over atomic details, the effective potentials governing CG degrees of freedom necessarily incorporate significant entropic contributions, which limit their transferability and complicate the treatment of thermodynamic properties. This work employs a dual-potential approach to consider the energetic and entropic contributions to effective interaction potentials for CG models. Specifically, we consider one- and three-site CG models for ortho-terphenyl (OTP) both above and below its glass transition. We employ the multiscale coarse-graining (MS-CG) variational principle to determine interaction potentials that accurately reproduce the structural properties of an all-atom (AA) model for OTP at each state point. We employ an energy-matching variational principle to determine an energy operator that accurately reproduces the intra- and inter-molecular energy of the AA model. While the MS-CG pair potentials are almost purely repulsive, the corresponding pair energy functions feature a pronounced minima that corresponds to contacting benzene rings. These energetic functions then determine an estimate for the entropic component of the MS-CG interaction potentials. These entropic functions accurately predict the MS-CG pair potentials across a wide range of liquid state points at constant density. Moreover, the entropic functions also predict pair potentials that quite accurately model the AA pair structure below the glass transition. Thus, the dual-potential approach appears a promising approach for modeling AA energetics, as well as for predicting the temperature-dependence of CG effective potentials.

A new one-site coarse-grained model for water: Bottom-up many-body projected water (BUMPer). II. Temperature transferability and structural properties at low temperature

A number of studies have constructed coarse-grained (CG) models of water to understand its anomalous properties. Most of these properties emerge at low temperatures, and an accurate CG model needs to be applicable to these low-temperature ranges. However, direct use of CG models parameterized from other temperatures, e.g., room temperature, encounters a problem known as transferability, as the CG potential essentially follows the form of the many-body CG free energy function. Therefore, temperature-dependent changes to CG interactions must be accounted for. The collective behavior of water at low temperature is generally a many-body process, which often motivates the use of expensive many-body terms in the CG interactions. To surmount the aforementioned problems, we apply the Bottom-Up Many-Body Projected Water (BUMPer) CG model constructed from Paper I to study the low-temperature behavior of water. We report for the first time that the embedded three-body interaction enables BUMPer, despite its pairwise form, to capture the growth of ice at the ice/water interface with corroborating many-body correlations during the crystal growth. Furthermore, we propose temperature transferable BUMPer models that are indirectly constructed from the free energy decomposition scheme. Changes in CG interactions and corresponding structures are faithfully recapitulated by this framework. We further extend BUMPer to examine its ability to predict the structure, density, and diffusion anomalies by employing an alternative analysis based on structural correlations and pairwise potential forms to predict such anomalies. The presented analysis highlights the existence of these anomalies in the low-temperature regime and overcomes potential transferability problems.

Temperature and Phase Transferable Bottom-up Coarse-Grained Models

Despite the high fidelity of bottom-up coarse-grained (CG) approaches to recapitulate the structural correlations in atomistic simulations, the general use of bottom-up CG methods is limited because of the nontransferable nature of these CG models under different thermodynamic conditions. Because bottom-up CG potentials usually correspond to configuration-dependent free energies of the system, recent studies have focused on adjusting enthalpic or entropic contributions to account for issues with transferability. However, these approaches can require a manual adjustment of the CG interaction a priori and are usually limited to constant volume ensembles. To overcome these limitations, we construct temperature and phase transferable CG models under constant pressure by developing the ultra-coarse-graining (UCG) methodology in the mean-field limit. In the mean-field ansatz, an embedded semi-global order parameter recapitulates global changes to the system by automatically adjusting the effective CG interactions, thus bridging free energy decompositions with UCG theory. The method presented is designed to faithfully capture structural correlations under different thermodynamic conditions, using a single UCG model. Specifically, we test the applicability of the developed theory in three distinct cases: (1) different temperatures at constant pressure in liquids, (2) different temperatures across thermodynamic phases, and (3) liquid/vapor interfaces. We demonstrate that the systematic construction of both temperature and phase transferable bottom-up CG models is possible using this generalized UCG theory. Based on our findings, this approach significantly extends the transferability and applicability of the bottom-up CG theory and method.