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Register a new userExplaining classifiers to understand coarse-grained models
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Added by
Aleksander Durumeric
Publication date
2021
fields
Physics
and research's language is
English
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Bottom-up coarse-grained molecular dynamics models are parameterized using complex effective Hamiltonians. These models are typically optimized to approximate high dimensional data from atomistic simulations. In contrast, human validation of these models is often limited to low dimensional statistics that do not necessarily differentiate between the CG model and said atomistic simulations. We propose that explainable machine learning can directly convey high-dimensional error to scientists and use Shapley additive explanations do so in two coarse-grained protein models.
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Transitions between different conformational states are ubiquitous in proteins, being involved in signaling, catalysis and other fundamental activities in cells. However, modeling those processes is extremely difficult, due to the need of efficiently exploring a vast conformational space in order to seek for the actual transition path for systems whose complexity is already high in the steady states. Here we report a strategy that simplifies this task attacking the complexity on several sides. We first apply a minimalist coarse-grained model to Calmodulin, based on an empirical force field with a partial structural bias, to explore the transition paths between the apo-closed state and the Ca-bound open state of the protein. We then select representative structures along the trajectory based on a structural clustering algorithm and build a cleaned-up trajectory with them. We finally compare this trajectory with that produced by the online tool MinActionPath, by minimizing the action integral using a harmonic network model, and with that obtained by the PROMPT morphing method, based on an optimal mass transportation-type approach including physical constraints. The comparison is performed both on the structural and energetic level, using the coarse-grained and the atomistic force fields upon reconstruction. Our analysis indicates that this method returns trajectories capable of exploring intermediate states with physical meaning, retaining a very low computational cost, which can allow systematic and extensive exploration of the multi-stable proteins transition pathways.
Numerous molecular systems, including solutions, proteins, and composite materials, can be modeled using mixed-resolution representations, of which the quantum mechanics/molecular mechanics (QM/MM) approach has become the most widely used. However, the QM/MM approach often faces a number of challenges, including the slow sampling of the large configuration space for the MM part, the high cost of repetitive QM computations for changing coordinates of atoms in the MM surroundings, and a difficulty in providing a simple, qualitative interpretation of numerical results in terms of the influence of the molecular environment upon the active QM region. In this paper, we address these issues by combining QM/MM modeling with the methodology of bottom-up coarse-graining (CG) to provide the theoretical basis for a systematic quantum-mechanical/coarse-grained molecular mechanics (QM/CG-MM) mixed resolution approach. A derivation of the method is presented based on a combination of statistical mechanics and quantum mechanics, leading to an equation for the effective Hamiltonian of the QM part, a central concept in the QM/CG-MM theory. A detailed analysis of different contributions to the effective Hamiltonian from electrostatic, induction, dispersion and exchange interactions between the QM part and the surroundings is provided, serving as a foundation for a potential hierarchy of QM/CG-MM methods varying in their accuracy and computational cost. A relationship of the QM/CG-MM methodology to other mixed resolution approaches is also discussed.
A coarse-grained simulation model eliminates microscopic degrees of freedom and represents a polymer by a simplified structure. A priori, two classes of coarse-grained models may be distinguished: those which are designed for a specific polymer and reflect the underlying atomistic details to some extent, and those which retain only the most basic features of a polymer chain (chain connectivity, short-range excluded-volume interactions, etc.). In this review we mainly focus on the second class of generic polymer models, while the first class of specific coarse-grained models is only touched upon briefly.
One can think of some physical evolutions as being the emergent-effective result of a microscopic discrete model. Inspired by classical coarse-graining procedures, we provide a simple procedure to coarse-grain color-blind quantum cellular automata that follow Goldilocks rules. The procedure consists in (i) space-time grouping the quantum cellular automaton (QCA) in cells of size $N$; (ii) projecting the states of a cell onto its borders, connecting them with the fine dynamics; (iii) describing the overall dynamics by the border states, that we call signals; and (iv) constructing the coarse-grained dynamics for different sizes $N$ of the cells. A byproduct of this simple toy-model is a general discrete analog of the Stokes law. Moreover we prove that in the spacetime limit, the automaton converges to a Dirac free Hamiltonian. The QCA we introduce here can be implemented by present-day quantum platforms, such as Rydberg arrays, trapped ions, and superconducting qbits. We hope our study can pave the way to a richer understanding of those systems with limited resolution.
We show that the full dynamical freedom of the well known Szekeres models allows for the description of elaborated 3--dimensional networks of cold dark matter structures (over--densities and/or density voids) undergoing pancake collapse. By reducing Einsteins field equations to a set of evolution equations, which themselves reduce in the linear limit to evolution equations for linear perturbations, we determine the dynamics of such structures, with the spatial comoving location of each structure uniquely specified by standard early Universe initial conditions. By means of a representative example we examine in detail the density contrast, the Hubble flow and peculiar velocities of structures that evolved, from linear initial data at the last scattering surface, to fully non--linear 10--20 Mpc. scale configurations today. To motivate further research, we provide a qualitative discussion on the connection of Szekeres models with linear perturbations and the pancake collapse of the Zeldovich approximation. This type of structure modelling provides a coarse grained -- but fully relativistic non--linear and non--perturbative -- description of evolving large scale cosmic structures before their virialisation, and as such it has an enormous potential for applications in cosmological research.
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