Computation Of Partition Functions Research Articles

Ising model partition-function computation as a weighted counting problem.

While the Ising model is most often used to understand physical phenomena, its natural connection to combinatorial reasoning also makes it one of the best models to probe complex systems in science and engineering. We bring a computational lens to the study of Ising models, where our computer-science perspective is twofold: On the one hand, we show that partition function computation (#Ising) can be reduced to weighted model counting (WMC). This enables us to take off-the-shelf model counters and apply them to #Ising. We show that one model counter (TensorOrder) outperforms state-of-the-art tools for #Ising on midsize and topologically unstructured instances, suggesting the tool would be a useful addition to a portfolio of partition function solvers. On the other hand, we consider the computational complexity of #Ising and relate it to the logic-based counting of constraint-satisfaction problems or #CSP. We show that known dichotomy results for #CSP give an easy proof of the hardness of #Ising and provide intuition on where the difficulty of #Ising comes from.

On the computation of moments in the Super-Transition-Arrays model for radiative opacity calculations

In the Super-Transition-Array statistical method for the computation of radiative opacity of hot dense matter, the moments of the absorption or emission features involve partition functions with reduced degeneracies, occurring through the calculation of averages of products of subshell populations. In the present work, we discuss several aspects of the computation of such peculiar partition functions, insisting on the precautions that must be taken in order to avoid numerical difficulties. In a previous work, we derived a formula for supershell partition functions, which takes the form of a functional of the distribution of energies within the supershell and allows for fast and accurate computations, truncating the number of terms in the expansion. The latter involves coefficients for which we obtained a recursion relation and an explicit formula. We show that such an expansion can be combined with the recurrence relation for shifted partition functions. We also propose, neglecting the effect of fine structure as a first step, a positive-definite formula for the Super-Transition-Array moments of any order, providing an insight into the asymmetry and sharpness of the latter. The corresponding formulas are free of alternating sums. Several ways to speed up the calculations are also presented.

Computing equilibrium free energies through a nonequilibrium quench.

Many methods to accelerate sampling of molecular configurations are based on the idea that temperature can be used to accelerate rare transitions. These methods typically compute equilibrium properties at a target temperature using reweighting or through Monte Carlo exchanges between replicas at higher temperatures. A recent paper [G. M. Rotskoff and E. Vanden-Eijnden, Phys. Rev. Lett. 122, 150602 (2019)] demonstrated that accurate equilibrium densities of states can also be computed through a nonequilibrium "quench" process, where sampling is performed at a higher temperature to encourage rapid mixing and then quenched to lower energy states with dissipative dynamics. Here, we provide an implementation of the quench dynamics in LAMMPS and evaluate a new formulation of nonequilibrium estimators for the computation of partition functions or free energy surfaces (FESs) of molecular systems. We show that the method is exact for a minimal model of N-independent harmonic springs and use these analytical results to develop heuristics for the amount of quenching required to obtain accurate sampling. We then test the quench approach on alanine dipeptide, where we show that it gives an FES that is accurate near the most stable configurations using the quench approach but disagrees with a reference umbrella sampling calculation in high FE regions. We then show that combining quenching with umbrella sampling allows the efficient calculation of the free energy in all regions. Moreover, by using this combined scheme, we obtain the FES across a range of temperatures at no additional cost, making it much more efficient than standard umbrella sampling if this information is required. Finally, we discuss how this approach can be extended to solute tempering and demonstrate that it is highly accurate for the case of solvated alanine dipeptide without any additional modifications.

Equivariant localization and holography

We discuss the theory of equivariant localization focussing on applications relevant for holography. We consider geometries comprising compact and non-compact toric orbifolds, as well as more general non-compact toric Calabi–Yau singularities. A key object in our constructions is the equivariant volume, for which we describe two methods of evaluation: the Berline–Vergne fixed point formula and the Molien–Weyl formula, supplemented by the Jeffrey–Kirwan prescription. We present two applications in supersymmetric field theories. Firstly, we describe a method for integrating the anomaly polynomial of SCFTs on compact toric orbifolds. Secondly, we discuss equivariant orbifold indices that are expected to play a key role in the computation of supersymmetric partition functions. In the context of supergravity, we propose that the equivariant volume can be used to characterize universally the geometry of a large class of supersymmetric solutions. As an illustration, we employ equivariant localization to prove the factorization in gravitational blocks of various supergravity free energies, recovering previous results as well as obtaining generalizations.

Quantum Chern–Simons Theories on Cylinders: BV-BFV Partition Functions

We compute partition functions of Chern–Simons type theories for cylindrical spacetimes I times Sigma , with I an interval and dim Sigma = 4l+2, in the BV-BFV formalism (a refinement of the Batalin–Vilkovisky formalism adapted to manifolds with boundary and cutting–gluing). The case dim Sigma = 0 is considered as a toy example. We show that one can identify—for certain choices of residual fields—the “physical part” (restriction to degree zero fields) of the BV-BFV effective action with the Hamilton–Jacobi action computed in the companion paper (Cattaneo et al., Constrained systems, generalized Hamilton–Jacobi actions, and quantization, arXiv:2012.13270), without any quantum corrections. This Hamilton–Jacobi action is the action functional of a conformal field theory on Sigma . For dim Sigma = 2, this implies a version of the CS-WZW correspondence. For dim Sigma = 6, using a particular polarization on one end of the cylinder, the Chern–Simons partition function is related to Kodaira–Spencer gravity (a.k.a. BCOV theory); this provides a BV-BFV quantum perspective on the semiclassical result by Gerasimov and Shatashvili.

Selberg trace formula in hyperbolic band theory.

We apply Selberg's trace formula to solve problems in hyperbolic band theory, a recently developed extension of Bloch theory to model band structures on experimentally realized hyperbolic lattices. For this purpose we incorporate the higher-dimensional crystal momentum into the trace formula and evaluate the summation for periodic orbits on the Bolza surface of genus two. We apply the technique to compute partition functions on the Bolza surface and propose an approximate relation between the lowest bands on the Bolza surface and on the {8,3} hyperbolic lattice. We discuss the role of automorphism symmetry and its manifestation in the trace formula.

Computing partition functions in the one-clean-qubit model

We present a method to approximate partition functions of quantum systems using mixed-state quantum computation. For positive-semidefinite Hamiltonians, our method has an expected running-time that is almost linear in ${[M/({\ensuremath{\epsilon}}_{\mathrm{rel}}\mathcal{Z})]}^{2}$, where $M$ is the dimension of the quantum system, $\mathcal{Z}$ is the partition function, and ${\ensuremath{\epsilon}}_{\mathrm{rel}}$ is the relative precision. It is based on approximations of the exponential operator as linear combinations of certain operators related to block-encoding of Hamiltonians or Hamiltonian evolutions. The trace of each operator is estimated using a standard algorithm in the one-clean-qubit model. For large values of $\mathcal{Z}$, our method may run faster than exact classical methods, whose complexities are polynomial in $M$. We also prove that a version of the partition function estimation problem within additive error is complete for the so-called DQC1 complexity class, suggesting that our method provides a superpolynomial speedup for certain parameter values. To attain a desired relative precision, we develop a classical procedure based on a sequence of approximations within predetermined additive errors that may be of independent interest.

Ambiguities in the local thermal behavior of the scalar radiation in one-dimensional boxes

This paper reports certain ambiguities in the calculation of the ensemble average $\left<T_\mu{}_\nu\right>$ of the stress-energy-momentum tensor of an arbitrarily coupled massless scalar field in one-dimensional boxes in flat spacetime. The study addresses a box with periodic boundary condition (a circle) and boxes with reflecting edges (with Dirichlet's or Neumann's boundary conditions at the endpoints). The expressions for $\left<T^\mu{}^\nu\right>$ are obtained from finite-temperature Green functions. In an appendix, in order to control divergences typical of two dimensions, these Green functions are calculated for related backgrounds with arbitrary number of dimensions and for scalar fields of arbitrary mass, and specialized in the text to two dimensions and for massless fields. The ambiguities arise due to the presence in $\left<T^\mu{}^\nu\right>$ of double series that are not absolutely convergent. The order in which the two associated summations are evaluated matters, leading to two different thermodynamics for each type of box. In the case of a circle, it is shown that the ambiguity corresponds to the classic controversy in the literature whether or not zero mode contributions should be taken into account in computations of partition functions. In the case of boxes with reflecting edges, it results that one of the thermodynamics corresponds to a total energy (obtained by integrating the non homogeneous energy density over space) that does not depend on the curvature coupling parameter $\xi$ as expected; whereas the other thermodynamics curiously corresponds to a total energy that does depend on $\xi$. Thermodynamic requirements (such as local and global stability) and their restrictions to the values of $\xi$ are considered.

Rapid prediction of crucial hotspot interactions for icosahedral viral capsid self-assembly by energy landscape atlasing validated by mutagenesis.

Icosahedral viruses are under a micrometer in diameter, their infectious genome encapsulated by a shell assembled by a multiscale process, starting from an integer multiple of 60 viral capsid or coat protein (VP) monomers. We predict and validate inter-atomic hotspot interactions between VP monomers that are important for the assembly of 3 types of icosahedral viral capsids: Adeno Associated Virus serotype 2 (AAV2) and Minute Virus of Mice (MVM), both T = 1 single stranded DNA viruses, and Bromo Mosaic Virus (BMV), a T = 3 single stranded RNA virus. Experimental validation is by in-vitro, site-directed mutagenesis data found in literature. We combine ab-initio predictions at two scales: at the interface-scale, we predict the importance (cruciality) of an interaction for successful subassembly across each interface between symmetry-related VP monomers; and at the capsid-scale, we predict the cruciality of an interface for successful capsid assembly. At the interface-scale, we measure cruciality by changes in the capsid free-energy landscape partition function when an interaction is removed. The partition function computation uses atlases of interface subassembly landscapes, rapidly generated by a novel geometric method and curated opensource software EASAL (efficient atlasing and search of assembly landscapes). At the capsid-scale, cruciality of an interface for successful assembly of the capsid is based on combinatorial entropy. Our study goes all the way from resource-light, multiscale computational predictions of crucial hotspot inter-atomic interactions to validation using data on site-directed mutagenesis' effect on capsid assembly. By reliably and rapidly narrowing down target interactions, (no more than 1.5 hours per interface on a laptop with Intel Core i5-2500K @ 3.2 Ghz CPU and 8GB of RAM) our predictions can inform and reduce time-consuming in-vitro and in-vivo experiments, or more computationally intensive in-silico analyses.

Exact results and Schur expansions in quiver Chern-Simons-matter theories

We study several quiver Chern-Simons-matter theories on the three-sphere, combining the matrix model formulation with a systematic use of Mordell’s integral, computing partition functions and checking dualities. We also consider Wilson loops in ABJ(M) theories, distinguishing between typical (long) and atypical (short) representations and focusing on the former. Using the Berele-Regev factorization of supersymmetric Schur polynomials, we express the expectation value of the Wilson loops in terms of sums of observables of two factorized copies of U(N ) pure Chern-Simons theory on the sphere. Then, we use the Cauchy identity to study the partition functions of a number of quiver Chern-Simons-matter models and the result is interpreted as a perturbative expansion in the parameters tj = −e2πmj , where mj are the masses. Through the paper, we incorporate different generalizations, such as deformations by real masses and/or Fayet-Iliopoulos parameters, the consideration of a Romans mass in the gravity dual, and adjoint matter.

Optimized recursion relation for the computation of partition functions in the superconfiguration approach

Partition functions of a canonical ensemble of non-interacting bound electrons are a key ingredient of the super-transition-array approach to the computation of radiative opacity. A few years ago, we published a robust and stable recursion relation for the calculation of such partition functions. In this paper, we propose an optimization of the latter method and explain how to implement it in practice. The formalism relies on the evaluation of elementary symmetric polynomials, which opens the way to further improvements.

Erasure machine: Inverse Ising inference from reweighting of observation frequencies.

Maximum likelihood estimation (MLE) is fundamental to system inference for stochastic systems. In some generality, MLE will converge to the correct model in the infinite data limit. In the context of physical approaches to system inference, such as Boltzmann machines, MLE requires the arduous computation of partition functions summing over all configurations, both observed and unobserved. We present a conceptually transparent data-driven inference computation based on a reweighting of observed configuration frequencies that allows us to recast the inference problem as a simpler calculation. Modeling our approach on the high-temperature limit of statistical physics, we reweight the frequencies of observed configurations by multiplying with reciprocals of Boltzmann weights and update the Boltzmann weights iteratively to make these products close to the high-temperature limit of the Boltzmann weights. This converts the required partition function computation in the reweighted MLE to a tractable leading-order high-temperature term. We show that this is a convex optimization at each step. Then, for systems with a large number of degrees of freedom where other approaches are intractable, we demonstrate that this data-driven algorithm gives accurate inference with both synthetic data and two real-world examples.

Three-dimensional 𝒩 = 2 supersymmetric gauge theories and partition functions on Seifert manifolds: A review

We give a pedagogical introduction to the study of supersymmetric partition functions of 3D [Formula: see text] supersymmetric Chern–Simons-matter theories (with an [Formula: see text]-symmetry) on half-BPS closed three-manifolds — including [Formula: see text], [Formula: see text], and any Seifert three-manifold. Three-dimensional gauge theories can flow to nontrivial fixed points in the infrared. In the presence of 3D [Formula: see text] supersymmetry, many exact results are known about the strongly-coupled infrared, due in good part to powerful localization techniques. We review some of these techniques and emphasize some more recent developments, which provide a simple and comprehensive formalism for the exact computation of half-BPS observables on closed three-manifolds (partition functions and correlation functions of line operators). Along the way, we also review simple examples of 3D infrared dualities. The computation of supersymmetric partition functions provides exceedingly precise tests of these dualities.

Cost function network-based design of protein-protein interactions: predicting changes in binding affinity.

Accurate and economic methods to predict change in protein binding free energy upon mutation are imperative to accelerate the design of proteins for a wide range of applications. Free energy is defined by enthalpic and entropic contributions. Following the recent progresses of Artificial Intelligence-based algorithms for guaranteed NP-hard energy optimization and partition function computation, it becomes possible to quickly compute minimum energy conformations and to reliably estimate the entropic contribution of side-chains in the change of free energy of large protein interfaces. Using guaranteed Cost Function Network algorithms, Rosetta energy functions and Dunbrack's rotamer library, we developed and assessed EasyE and JayZ, two methods for binding affinity estimation that ignore or include conformational entropic contributions on a large benchmark of binding affinity experimental measures. If both approaches outperform most established tools, we observe that side-chain conformational entropy brings little or no improvement on most systems but becomes crucial in some rare cases. as open-source Python/C++ code at sourcesup.renater.fr/projects/easy-jayz. Supplementary data are available at Bioinformatics online.

New approach to canonical partition functions computation in Nf=2 lattice QCD at finite baryon density

We propose and test a new approach to computation of canonical partition functions in lattice QCD at finite density. We suggest a few steps procedure. We first compute numerically the quark number density for imaginary chemical potential $i\mu_{qI}$. Then we restore the grand canonical partition function for imaginary chemical potential using fitting procedure for the quark number density. Finally we compute the canonical partition functions using high precision numerical Fourier transformation. Additionally we compute the canonical partition functions using known method of the hopping parameter expansion and compare results obtained by two methods in the deconfining as well as in the confining phases. The agreement between two methods indicates the validity of the new method. Our numerical results are obtained in two flavor lattice QCD with clover improved Wilson fermions.

Study of lattice QCD at finite chemical potential using the canonical ensemble approach

New approach to computation of canonical partition functions in $N_f=2$ lattice QCD is presented. We compare results obtained by new method with results obtained by known method of hopping parameter expansion. We observe agreement between two methods indicating validity of the new method. We use results for the number density obtained in the confining and deconfining phases at imaginary chemical potential to determine the phase transition line at real chemical potential.

Taming supersymmetric defects in 3d–3d correspondence

We study knots in 3d Chern–Simons theory with complex gauge group , in the context of its relation with 3d theory (the so-called 3d–3d correspondence). The defect has either co-dimension 2 or co-dimension 4 inside the 6d theory, which is compactified on a 3-manifold . We identify such defects in various corners of the 3d–3d correspondence, namely in 3d CS theory, in 3d theory, in 5d super Yang–Mills theory, and in the M-theory holographic dual. We can make quantitative checks of the 3d–3d correspondence by computing partition functions at each of these theories. This Letter is a companion to a longer paper [], which contains more details and more results.

Long, partial-short, and special conformal fields

In the framework of metric-like approach, totally symmetric arbitrary spin bosonic conformal fields propagating in flat space-time are studied. Depending on the values of conformal dimension, spin, and dimension of space-time, we classify all conformal field as long, partial-short, short, and special conformal fields. An ordinary-derivative (second-derivative) Lagrangian formulation for such conformal fields is obtained. The ordinary-derivative Lagrangian formulation is realized by using double-traceless gauge fields, Stueckelberg fields, and auxiliary fields. Gauge-fixed Lagrangian invariant under global BRST transformations is obtained. The gauge-fixed BRST Lagrangian is used for the computation of partition functions for all conformal fields. Using the result for the partition functions, numbers of propagating D.o.F for the conformal fields are also found.

Quantum speedup of Monte Carlo methods.

Monte Carlo methods use random sampling to estimate numerical quantities which are hard to compute deterministically. One important example is the use in statistical physics of rapidly mixing Markov chains to approximately compute partition functions. In this work, we describe a quantum algorithm which can accelerate Monte Carlo methods in a very general setting. The algorithm estimates the expected output value of an arbitrary randomized or quantum subroutine with bounded variance, achieving a near-quadratic speedup over the best possible classical algorithm. Combining the algorithm with the use of quantum walks gives a quantum speedup of the fastest known classical algorithms with rigorous performance bounds for computing partition functions, which use multiple-stage Markov chain Monte Carlo techniques. The quantum algorithm can also be used to estimate the total variation distance between probability distributions efficiently.

Computing the partition function for graph homomorphisms with multiplicities

We consider a refinement of the partition function of graph homomorphisms and present a quasi-polynomial algorithm to compute it in a certain domain. As a corollary, we obtain quasi-polynomial algorithms for computing partition functions for independent sets, perfect matchings, Hamiltonian cycles and dense subgraphs in graphs as well as for graph colorings. This allows us to tell apart in quasi-polynomial time graphs that are sufficiently far from having a structure of a given type (i.e., independent set of a given size, Hamiltonian cycle, etc.) from graphs that have sufficiently many structures of that type, even when the probability to hit such a structure at random is exponentially small.