Quantum Computing for Molecular Biology

Molecular biology and biochemistry interpret microscopic processes in the living world in terms of molecular structures and their interactions, which are quantum mechanical by their very nature. Whereas the theoretical foundations of these interactions are very well established, the computational solution of the relevant quantum mechanical equations is very hard. However, much of molecular function in biology can be understood in terms of classical mechanics, where the interactions of electrons and nuclei have been mapped onto effective classical surrogate potentials that model the interaction of atoms or even larger entities. The simple mathematical structure of these potentials offers huge computational advantages; however, this comes at the cost that all quantum correlations and the rigorous many-particle nature of the interactions are omitted. In this work, we discuss how quantum computation may advance the practical usefulness of the quantum foundations of molecular biology by offering computational advantages for simulations of biomolecules. We not only discuss typical quantum mechanical problems of the electronic structure of biomolecules in this context, but also consider the dominating classical problems (such as protein folding and drug design) as well as data-driven approaches of bioinformatics and the degree to which they might become amenable to quantum simulation and quantum computation.Comment: 76 pages, 7 figure

Flexible DMRG-based framework for anharmonic vibrational calculations

We present a novel formulation of the vibrational density matrix renormalization group (vDMRG) algorithm tailored to strongly anharmonic molecules described by general high-dimensional model representations of potential energy surfaces. For this purpose, we extend the vDMRG framework to support vibrational Hamiltonians expressed in the so-called $n$-mode second-quantization formalism. The resulting $n$-mode vDMRG method offers full flexibility with respect to both the functional form of the PES and the choice of single-particle basis set. We leverage this framework to apply, for the first time, vDMRG based on an anharmonic modal basis set optimized with the vibrational self-consistent field algorithm on an on-the-fly constructed PES. We also extend the $n$-mode vDMRG framework to include excited-state targeting algorithms in order to efficiently calculate anharmonic transition frequencies. We demonstrate the capabilities of our novel $n$-mode vDMRG framework for methyloxirane, a challenging molecule with 24 coupled vibrational modes.Comment: 46 pages, 6 figures, 2 table

Symmetry-Projected Nuclear-Electronic Hartree-Fock: Eliminating Rotational Energy Contamination

We present a symmetry projection technique for enforcing rotational and parity symmetries in nuclear-electronic Hartree-Fock wave functions, which treat electrons and nuclei on equal footing. The molecular Hamiltonian obeys rotational and parity-inversion symmetries, which are, however, broken by expanding in Gaussian basis sets that are fixed in space. We generate a trial wave function with the correct symmetry properties by projecting the wave function onto representations of the three-dimensional rotation group, i.e., the special orthogonal group in three dimensions SO(3). As a consequence, the wave function becomes an eigenfunction of the angular momentum operator which (i) eliminates the contamination of the ground state wave function by highly excited rotational states arising from the broken rotational symmetry, and (ii) enables the targeting of specific rotational states of the molecule. We demonstrate the efficiency of the symmetry projection technique by calculating energies of the low-lying rotational states of the H$_2$ and H$_3^+$ molecules.Comment: 37 pages, 3 table

Simulation Of Accurate Vibrationally Resolved Electronic Spectra: The Integrated Time-dependent And Time-independent Framework

Two parallel theories including Franck–Condon, Herzberg–Teller and Duschinsky (i.e., mode mixing) effects, allowing different approximations for the description of excited state PES have been developed in order to simulate realistic, asymmetric, electronic spectra line-shapes taking into account the vibrational structure: the so-called sum-over-states or time-independent (TI) method and the alternative time-dependent (TD) approach, which exploits the properties of the Fourier transform. The integrated TI-TD procedure included within a general purpose QM code [1,2], allows to compute one photon absorption, fluorescence, phosphorescence, electronic circular dichroism, circularly polarized luminescence and resonance Raman spectra. Combining both approaches, which use a single set of starting data, permits to profit from their respective advantages and minimize their respective limits: the time-dependent route automatically includes all vibrational states and, possibly, temperature effects, while the time-independent route allows to identify and assign single vibronic transitions. Interpretation, analysis and assignment of experimental spectra based on integrated TI-TD vibronic computations will be illustrated for challenging cases of medium-sized open-shell systems in the gas and condensed phases with inclusion of leading anharmonic effects. 1. V. Barone, A. Baiardi, M. Biczysko, J. Bloino, C. Cappelli, F. Lipparini Phys. Chem. Chem. Phys, 14, 12404, (2012) 2. A. Baiardi, V. Barone, J. Bloino J. Chem. Theory Comput., 9, 4097–4115 (2013

Tensor Network States for Vibrational Spectroscopy

This review elaborates on the foundation, the advantages, and the prospects of tensor network representations for quantum states in vibrational spectroscopy. The focus is on the recently introduced matrix product state decomposition of nuclear quantum states and its optimization by the density matrix renormalization group algorithm.Comment: 65 pages, 20 figure