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DOE OSTI2021

Ab initio molecular dynamics on quantum computers

Ab initio molecular dynamics (AIMD) is a valuable technique for studying molecules and materials at finite temperatures where the nuclei evolve on potential energy surfaces obtained from accurate electronic structure calculations. In this work, we present an approach to running AIMD simulations on noisy intermediate-scale quantum (NISQ)-era quantum computers. The electronic energies are calculated on a quantum computer using the variational quantum eigensolver (VQE) method. Algorithms for computation of analytical gradients entirely on a quantum computer require quantum fault-tolerant hardware, which is beyond NISQ-era. Therefore, we compute the energy gradients numerically using finite differences, the Hellmann-Feynman theorem, and a correlated sampling technique. This method only requires additional classical calculations of electron integrals for each degree of freedom without any additional computations on a quantum computer beyond the initial VQE run. As a proof of concept, AIMD simulations are demonstrated for the H-2 molecule on IBM quantum devices. In addition, we demonstrate the validity of the method for larger molecules using full configuration interaction wave functions. As quantum hardware and noise mitigation techniques continue to improve, the method can be utilized for studying larger molecular systems.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

Quantum Electrodynamics Coupled-Cluster at Scale: High-Performance Implementation for Complex Systems

Coupled-cluster theory (CC) is a highly accurate and versatile method for simulating complex interactions within quantum systems. The extension of CC theory to model mixed electron-photon processes with quantum electrodynamics (QED) has improved our capability to predict cavity-modified chemistry, a field where photons are used as cost-effective and eco-friendly alternatives to catalyze/inhibit chemical reactions. However, calculations with CC methods, even without incorporating QED effects, are often prohibitively expensive. Simulations of larger systems require scalable infrastructures that exist for traditional CC methods but not for QED-CC methods. As such, we present a GPU-enabled, high-performance, open-source implementation of the quantum electrodynamics coupled-cluster method with single and double excitations (QED-CCSD) within the ExaChem quantum chemistry software package. ExaChem relies on the Tensor Algebra for Many-body Methods (TAMM) infrastructure: a parallel heterogeneous tensor library designed to achieve scalable performance on modern heterogeneous supercomputing platforms. Furthermore, we discuss theoretical foundations, algorithmic details, and numerical benchmarks to showcase the larger systems that ExaChem can simulate and how the integration of photonic degrees-of-freedom alters their ground-state properties.

Basis sets↗
DOE OSTI2017

Approximate solutions of acoustic 3D integral equation and their application to seismic modeling and full-waveform inversion

Over the recent decades, a number of fast approximate solutions of Lippmann–Schwinger equation, which are more accurate than classic Born and Rytov approximations, were proposed in the field of electromagnetic modeling. Those developments could be naturally extended to acoustic and elastic fields; however, until recently, they were almost unknown in seismology. This paper presents several solutions of this kind applied to acoustic modeling for both lossy and lossless media. We evaluated the numerical merits of those methods and provide an estimation of their numerical complexity. In our numerical realization we use the matrix-free implementation of the corresponding integral operator. We study the accuracy of those approximate solutions and demonstrate, that the quasi-analytical approximation is more accurate, than the Born approximation. Further, we apply the quasi-analytical approximation to the solution of the inverse problem. It is demonstrated that, this approach improves the estimation of the data gradient, comparing to the Born approximation. The developed inversion algorithm is based on the conjugate-gradient type optimization. Numerical model study demonstrates that the quasi-analytical solution significantly reduces computation time of the seismic full-waveform inversion. We also show how the quasi-analytical approximation can be extended to the case of elastic wavefield.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2018

Non-perturbative methodologies for low-dimensional strongly-correlated systems: From non-Abelian bosonization to truncated spectrum methods

We review two important non-perturbative approaches for extracting the physics of low-dimensional strongly correlated quantum systems. Firstly, we start by providing a comprehensive review of non-Abelian bosonization. This includes an introduction to the basic elements of conformal field theory as applied to systems with a current algebra, and we orient the reader by presenting a number of applications of non-Abelian bosonization to models with large symmetries. We then tie this technique into recent advances in the ability of cold atomic systems to realize complex symme-tries. Secondly, we discuss truncated spectrum methods for the numerical study of systems in one and two dimensions. For one-dimensional systems we provide the reader with considerable insight into the methodology by reviewing canonical applications of the technique to the Ising model (and its variants) and the sine-Gordon model. Following this we review recent work on the development of renormalization groups, both numerical and analytical, that alleviate the effects of truncating the spectrum. Using these technologies, we consider a number of applications to one-dimensional systems: properties of carbon nanotubes, quenches in the Lieb-Liniger model, 1+1D quantum chro-modynamics, as well as Landau-Ginzburg theories. In the final part we move our attention to consider truncated spectrum methods applied to two-dimensional systems. This involves combining truncated spectrum methods with matrix product state algorithms. Lastly, we describe applications of this method to two-dimensional systems of free fermions and the quantum Ising model, including their non-equilibrium dynamics.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2025

Orientation reversal and the Chern-Simons natural boundary

We show that the fundamental property of preservation of relations, underlying resurgent analysis, provides a new perspective on crossing a natural boundary, an important general problem in theoretical and mathematical physics. This reveals a deeper rigidity aspect of resurgence in a quantum field theory path integral. The physical context here is the non-perturbative completion of complex Chern-Simons theory that associates to a 3-manifold a collection of q-series invariants labeled by Spinc structures, for which crossing the natural boundary corresponds to orientation reversal of the 3-manifold. Our new resurgent perspective leads to a practical numerical algorithm that generates q-series which are dual to unary q-series composed of false theta functions. Until recently, these duals were only known in a limited number of cases, essentially based on Ramanujan’s mock theta functions, and the common belief was that the duals might not even exist in the general case. Resurgence analysis identifies as primary objects Mordell integrals: up to changes of variables, they are Laplace transforms of resurgent functions. Their unique Borel summed transseries decomposition on either side of the Stokes line is simply the unique decomposition into real and imaginary parts. In turn, the latter are combinations of unary q-series in terms of q and its modular counterpart $\overset{\sim }{q}$ , and are resurgent by construction. The Mordell integral is analytic across the natural boundary of the q and $\overset{\sim }{q}$ series, and uniqueness of a similar decomposition which preserves algebraic relations on the other side of the boundary defines the unique boundary crossing of the q series. We demonstrate that this continuation can be efficiently implemented numerically. In the cases where unique mock modular identities are known, they are found by this numerical procedure, but the procedure can go well beyond the known list of identities. A particularly interesting feature of the resurgent approach is that it reveals new aspects, and is very different from other known approaches based on indefinite theta series, Appell-Lerch sums, and representation theory of logarithmic vertex operator algebras.

Chern-Simons theories↗
DOE OSTI2018

Compressed sparse tensor based quadrature for vibrational quantum mechanics integrals

A new method for fast evaluation of high dimensional integrals arising in quantum mechanics is proposed. Here, the method is based on sparse approximation of a high dimensional function followed by a low-rank compression. In the first step, we interpret the high dimensional integrand as a tensor in a suitable tensor product space and determine its entries by a compressed sensing based algorithm using only a few function evaluations. Secondly, we implement a rank reduction strategy to compress this tensor in a suitable low-rank tensor format using standard tensor compression tools. This allows representing a high dimensional integrand function as a small sum of products of low dimensional functions. Finally, a low dimensional Gauss–Hermite quadrature rule is used to integrate this low-rank representation, thus alleviating the curse of dimensionality. Finally, numerical tests on synthetic functions, as well as on energy correction integrals for water and formaldehyde molecules demonstrate the efficiency of this method using very few function evaluations as compared to other integration strategies.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2016

Asymptotic and spectral analysis of the gyrokinetic-waterbag integro-differential operator in toroidal geometry

Achieving plasmas with good stability and confinement properties is a key research goal for magnetic fusion devices. The underlying equations are the Vlasov–Poisson and Vlasov–Maxwell (VPM) equations in three space variables, three velocity variables, and one time variable. Even in those somewhat academic cases where global equilibrium solutions are known, studying their stability requires the analysis of the spectral properties of the linearized operator, a daunting task. We have identified a model, for which not only equilibrium solutions can be constructed, but many of their stability properties are amenable to rigorous analysis. It uses a class of solution to the VPM equations (or to their gyrokinetic approximations) known as waterbag solutions which, in particular, are piecewise constant in phase-space. It also uses, not only the gyrokinetic approximation of fast cyclotronic motion around magnetic field lines, but also an asymptotic approximation regarding the magnetic-field-induced anisotropy: the spatial variation along the field lines is taken much slower than across them. Together, these assumptions result in a drastic reduction in the dimensionality of the linearized problem, which becomes a set of two nested one-dimensional problems: an integral equation in the poloidal variable, followed by a one-dimensional complex Schrödinger equation in the radial variable. We show here that the operator associated to the poloidal variable is meromorphic in the eigenparameter, the pulsation frequency. We also prove that, for all but a countable set of real pulsation frequencies, the operator is compact and thus behaves mostly as a finite-dimensional one. The numerical algorithms based on such ideas have been implemented in a companion paper [D. Coulette and N. Besse, “Numerical resolution of the global eigenvalue problem for gyrokinetic-waterbag model in toroidal geometry” (submitted)] and were found to be surprisingly close to those for the original gyrokinetic-Vlasov equations. The purpose of the present paper is to make these new ideas accessible to two readerships: applied mathematicians and plasma physicists.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2018

A note on the S-matrix bootstrap for the 2d O(N) bosonic model

In this work we apply the S-matrix bootstrap maximization program to the 2d bosonic O ( N ) integrable model which has N species of scalar particles of mass m and no bound states. Since in previous studies theories were defined by maximizing the coupling between particles and their bound states, the main problem appears to be to find what other functional can be used to define this model. Instead, we argue that the defining property of this integrable model is that it resides at a vertex of the convex space determined by the unitarity and crossing constraints. Thus, the integrable model can be found by maximizing any linear functional whose gradient points in the general direction of the vertex, namely within a cone determined by the normals to the faces intersecting at the vertex. This is a standard problem in applied mathematics, related to semi-definite programming and solvable by fast available numerical algorithms. The information provided by the numerical solution is enough to reproduce the known analytical solution without using integrability, namely the Yang-Baxter equation. This situation seems quite generic so we expect that other theories without continuous parameters can also be found by maximizing linear functionals in the convex space of allowed S-matrices.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2024

Physics-Reinforced Machine Learning Algorithms for Multiscale Closure Model Discovery

The central objective of this project was to address the challenge of modeling and simulating complex multiscale turbulence phenomena by leveraging physics-guided machine learning (PGML) and hybrid modeling approaches. By integrating physics-based methods with data-driven models, the research focused on achieving robust and scalable solutions for geophysical turbulence, enhancing numerical weather prediction and climate research tools. The project resulted in significant advancements in computational modeling paradigms, predictive tools for reduced-order modeling, and innovative algorithms for fluid dynamics.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2025

A time-parallel multiple-shooting method for large-scale quantum optimal control

Quantum optimal control plays a crucial role in quantum computing by providing the interface between compiler and hardware. Solving the optimal control problem is particularly challenging for multi-qubit gates, due to the exponential growth in computational complexity with the system's dimensionality and the deterioration of optimization convergence. To ameliorate the computational complexity of time-integration, this paper introduces a multiple-shooting approach in which the time domain is divided into multiple windows and the intermediate states at window boundaries are treated as additional optimization variables. Further, this enables parallel computation of state evolution across time-windows, significantly accelerating objective function and gradient evaluations. Since the initial state matrix in each window is only guaranteed to be unitary upon convergence of the optimization algorithm, the conventional gate trace infidelity is replaced by a generalized infidelity that is convex for non-unitary state matrices. Continuity of the state across window boundaries is enforced by equality constraints. A quadratic penalty optimization method is used to solve the constrained optimal control problem, and an efficient adjoint technique is employed to calculate the gradients in each iteration. We demonstrate the effectiveness of the proposed method through numerical experiments on quantum Fourier transform gates in systems with 2, 3, and 4 qubits, noting a speedup of 80x for evaluating the gradient in the 4-qubit case, highlighting the method's potential for optimizing control pulses in multi-qubit quantum systems.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2017

Model's sparse representation based on reduced mixed GMsFE basis methods

In this paper, we propose a model's sparse representation based on reduced mixed generalized multiscale finite element (GMsFE) basis methods for elliptic PDEs with random inputs. A typical application for the elliptic PDEs is the flow in heterogeneous random porous media. Mixed generalized multiscale finite element method (GMsFEM) is one of the accurate and efficient approaches to solve the flow problem in a coarse grid and obtain the velocity with local mass conservation. When the inputs of the PDEs are parameterized by the random variables, the GMsFE basis functions usually depend on the random parameters. This leads to a large number degree of freedoms for the mixed GMsFEM and substantially impacts on the computation efficiency. In order to overcome the difficulty, we develop reduced mixed GMsFE basis methods such that the multiscale basis functions are independent of the random parameters and span a low-dimensional space. To this end, a greedy algorithm is used to find a set of optimal samples from a training set scattered in the parameter space. Reduced mixed GMsFE basis functions are constructed based on the optimal samples using two optimal sampling strategies: basis-oriented cross-validation and proper orthogonal decomposition. Although the dimension of the space spanned by the reduced mixed GMsFE basis functions is much smaller than the dimension of the original full order model, the online computation still depends on the number of coarse degree of freedoms. To significantly improve the online computation, we integrate the reduced mixed GMsFE basis methods with sparse tensor approximation and obtain a sparse representation for the model's outputs. The sparse representation is very efficient for evaluating the model's outputs for many instances of parameters. To illustrate the efficacy of the proposed methods, we present a few numerical examples for elliptic PDEs with multiscale and random inputs. In particular, a two-phase flow model in random porous media is simulated by the proposed sparse representation method.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2022

Landau discriminants

Scattering amplitudes in quantum field theories have intricate analytic properties as functions of the energies and momenta of the scattered particles. In perturbation theory, their singularities are governed by a set of nonlinear polynomial equations, known as Landau equations, for each individual Feynman diagram. The singularity locus of the associated Feynman integral is made precise with the notion of the Landau discriminant, which characterizes when the Landau equations admit a solution. In order to compute this discriminant, we present approaches from classical elimination theory, as well as a numerical algorithm based on homotopy continuation. These methods allow us to compute Landau discriminants of various Feynman diagrams up to 3 loops, which were previously out of reach. For instance, the Landau discriminant of the envelope diagram is a reducible surface of degree 45 in the three-dimensional space of kinematic invariants. We investigate geometric properties of the Landau discriminant, such as irreducibility, dimension and degree. In particular, we find simple examples in which the Landau discriminant has codimension greater than one. Furthermore, we describe a numerical procedure for determining which parts of the Landau discriminant lie in the physical regions. In order to study degenerate limits of Landau equations and bounds on the degree of the Landau discriminant, we introduce Landau polytopes and study their facet structure. Finally, we provide an efficient numerical algorithm for the computation of the number of master integrals based on the connection to algebraic statistics.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2016

Modeling of diatomic molecule using the Morse potential and the Verlet algorithm

Performing molecular modeling usually uses special software for Molecular Dynamics (MD) such as: GROMACS, NAMD, JMOL etc. Molecular dynamics is a computational method to calculate the time dependent behavior of a molecular system. In this work, MATLAB was used as numerical method for a simple modeling of some diatomic molecules: HCl, H{sub 2} and O{sub 2}. MATLAB is a matrix based numerical software, in order to do numerical analysis, all the functions and equations describing properties of atoms and molecules must be developed manually in MATLAB. In this work, a Morse potential was generated to describe the bond interaction between the two atoms. In order to analyze the simultaneous motion of molecules, the Verlet Algorithm derived from Newton’s Equations of Motion (classical mechanics) was operated. Both the Morse potential and the Verlet algorithm were integrated using MATLAB to derive physical properties and the trajectory of the molecules. The data computed by MATLAB is always in the form of a matrix. To visualize it, Visualized Molecular Dynamics (VMD) was performed. Such method is useful for development and testing some types of interaction on a molecular scale. Besides, this can be very helpful for describing some basic principles of molecular interaction for educational purposes.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2017

Higher-order triangular spectral element method with optimized cubature points for seismic wavefield modeling

The mass-lumped method avoids the cost of inverting the mass matrix and simultaneously maintains spatial accuracy by adopting additional interior integration points, known as cubature points. To date, such points are only known analytically in tensor domains, such as quadrilateral or hexahedral elements. Thus, the diagonal-mass-matrix spectral element method (SEM) in non-tensor domains always relies on numerically computed interpolation points or quadrature points. However, only the cubature points for degrees 1 to 6 are known, which is the reason that we have developed a p-norm-based optimization algorithm to obtain higher-order cubature points. In this way, we obtain and tabulate new cubature points with all positive integration weights for degrees 7 to 9. The dispersion analysis illustrates that the dispersion relation determined from the new optimized cubature points is comparable to that of the mass and stiffness matrices obtained by exact integration. Simultaneously, the Lebesgue constant for the new optimized cubature points indicates its surprisingly good interpolation properties. As a result, such points provide both good interpolation properties and integration accuracy. The Courant–Friedrichs–Lewy (CFL) numbers are tabulated for the conventional Fekete-based triangular spectral element (TSEM), the TSEM with exact integration, and the optimized cubature-based TSEM (OTSEM). A complementary study demonstrates the spectral convergence of the OTSEM. A numerical example conducted on a half-space model demonstrates that the OTSEM improves the accuracy by approximately one order of magnitude compared to the conventional Fekete-based TSEM. In particular, the accuracy of the 7th-order OTSEM is even higher than that of the 14th-order Fekete-based TSEM. Furthermore, the OTSEM produces a result that can compete in accuracy with the quadrilateral SEM (QSEM). The high accuracy of the OTSEM is also tested with a non-flat topography model. In terms of computational efficiency, the OTSEM is more efficient than the Fekete-based TSEM, although it is slightly costlier than the QSEM when a comparable numerical accuracy is required. - Highlights: • Higher-order cubature points for degrees 7 to 9 are developed. • The effects of quadrature rule on the mass and stiffness matrices has been conducted. • The cubature points have always positive integration weights. • Freeing from the inversion of a wide bandwidth mass matrix. • The accuracy of the TSEM has been improved in about one order of magnitude.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2016

Modeling and simulation challenges pursued by the Consortium for Advanced Simulation of Light Water Reactors (CASL)

The Consortium for the Advanced Simulation of Light Water Reactors (CASL), the first Energy Innovation Hub of the Department of Energy, was established in 2010 with the goal of providing modeling and simulation (M&S) capabilities that support and accelerate the improvement of nuclear energy's economic competitiveness and the reduction of spent nuclear fuel volume per unit energy, and all while assuring nuclear safety. To accomplish this requires advances in M&S capabilities in radiation transport, thermal-hydraulics, fuel performance and corrosion chemistry. To focus CASL's R&D, industry challenge problems have been defined, which equate with long standing issues of the nuclear power industry that M&S can assist in addressing. To date CASL has developed a multi-physics “core simulator” based upon pin-resolved radiation transport and subchannel (within fuel assembly) thermal-hydraulics, capitalizing on the capabilities of high performance computing. CASL's fuel performance M&S capability can also be optionally integrated into the core simulator, yielding a coupled multi-physics capability with untapped predictive potential. Material models have been developed to enhance predictive capabilities of fuel clad creep and growth, along with deeper understanding of zirconium alloy clad oxidation and hydrogen pickup. Understanding of corrosion chemistry (e.g., CRUD formation) has evolved at all scales: micro, meso and macro. CFD R&D has focused on improvement in closure models for subcooled boiling and bubbly flow, and the formulation of robust numerical solution algorithms. For multiphysics integration, several iterative acceleration methods have been assessed, illuminating areas where further research is needed. Finally, uncertainty quantification and data assimilation techniques, based upon sampling approaches, have been made more feasible for practicing nuclear engineers via R&D on dimensional reduction and biased sampling. Industry adoption of CASL's evolving M&S capabilities, which is in progress, will assist in addressing long-standing and future operational and safety challenges of the nuclear industry. - Highlights: • Complexity of physics based modeling of light water reactor cores being addressed. • Capability developed to help address problems that have challenged the nuclear power industry. • Simulation capabilities that take advantage of high performance computing developed.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗
DOE OSTI2023

Scalable generalized screening for high-order terms in the many-body expansion: Algorithm, open-source implementation, and demonstration

The many-body expansion lies at the heart of numerous fragment-based methods that are intended to sidestep the nonlinear scaling of ab initio quantum chemistry, making electronic structure calculations feasible in large systems. In principle, inclusion of higher-order n-body terms ought to improve the accuracy in a controllable way, but unfavorable combinatorics often defeats this in practice and applications with n ≥ 4 are rare. Here, we outline an algorithm to overcome this combinatorial bottleneck, based on a bottom-up approach to energy-based screening. This is implemented within a new open-source software application (“Fragme∩t”), which is integrated with a lightweight semi-empirical method that is used to cull subsystems, attenuating the combinatorial growth of higher-order terms in the graph that is used to manage the calculations. This facilitates applications of unprecedented size, and we report four-body calculations in (H2O)64 clusters that afford relative energies within 0.1 kcal/mol/monomer of the supersystem result using less than 10% of the unique subsystems. We also report n-body calculations in (H2O)20 clusters up to n = 8, at which point the expansion terminates naturally due to screening. These are the largest n-body calculations reported to date using ab initio electronic structure theory, and they confirm that high-order n-body terms are mostly artifacts of basis-set superposition error.

Chemistry↗
DOE OSTI2018

Generalized, Energy-conserving Numerical Simulations of Particles in General Relativity. I. Time-like and Null Geodesics

The numerical integration of particle trajectories in curved spacetimes is fundamental for obtaining realistic models of the particle dynamics around massive compact objects such as black holes and neutron stars. Generalized algorithms capable of handling generic metrics are needed for studies of both standard (Schwarzschild and Kerr metrics) and nonstandard (e.g., Schwarzschild metric plus nonclassical perturbations or multiple black hole metrics) spacetimes. The most commonly employed explicit numerical schemes (e.g., Runge–Kutta) are incapable of producing highly accurate results at critical points, e.g., in the regions close to the event horizon where gravity causes extreme curvature of the spacetime, at an acceptable computational cost. In this work we describe a generalized algorithm for the numerical integration of time-like (massive particles) and null (photons) geodesics in any given 3 + 1 split spacetime. We introduce a new, exactly energy-conserving implicit integration scheme based on the preservation of the underlying Hamiltonian, and we compare its properties with a standard fourth-order Runge–Kutta explicit scheme and an implicit midpoint scheme. We test the numerical performance of the three schemes against analytic solutions of particle and photon orbits in Schwarzschild and Kerr spacetimes. We additionally prove the versatility of our framework in handling more exotic metrics, such as Morris–Thorne wormholes and quantum-perturbed Schwarzschild black holes. The generalized method is also discussed in the perspective of future extensions to more complex particle dynamics, e.g., the addition of the Lorentz force acting on charged particles, which allows for test particle diagnostics in GRMHD simulations.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2023

PTM‐Psi : A python package to facilitate the computational investigation of p ost‐ t ranslational m odification on p rotein s tructures and their i mpacts on dynamics and functions

Abstract Post‐translational modification (PTM) of a protein occurs after it has been synthesized from its genetic template, and involves chemical modifications of the protein's specific amino acid residues. Despite of the central role played by PTM in regulating molecular interactions, particularly those driven by reversible redox reactions, it remains challenging to interpret PTMs in terms of protein dynamics and function because there are numerous combinatorially enormous means for modifying amino acids in response to changes in the protein environment. In this study, we provide a workflow that allows users to interpret how perturbations caused by PTMs affect a protein's properties, dynamics, and interactions with its binding partners based on inferred or experimentally determined protein structure. This Python‐based workflow, called PTM‐Psi , integrates several established open‐source software packages, thereby enabling the user to infer protein structure from sequence, develop force fields for non‐standard amino acids using quantum mechanics, calculate free energy perturbations through molecular dynamics simulations, and score the bound complexes via docking algorithms. Using the S ‐nitrosylation of several cysteines on the GAP2 protein as an example, we demonstrated the utility of PTM‐Psi for interpreting sequence–structure–function relationships derived from thiol redox proteomics data. We demonstrate that the S ‐nitrosylated cysteine that is exposed to the solvent indirectly affects the catalytic reaction of another buried cysteine over a distance in GAP2 protein through the movement of the two ligands. Our workflow tracks the PTMs on residues that are responsive to changes in the redox environment and lays the foundation for the automation of molecular and systems biology modeling.

59 BASIC BIOLOGICAL SCIENCES↗