Stochastic approach to molecular interactions and computational theory of metabolic and genetic regulations

Binding and unbinding of ligands to specific sites of a macromolecule are one of the most elementary molecular interactions inside the cell that embody the computational processes of biological regulations. The interaction between transcription factors and the operators of genes and that between ligands and binding sites of allosteric enzymes are typical examples of such molecular interactions. In order to obtain the general mathematical framework of biological regulations, we formulate these interactions as finite Markov processes and establish a computational theory of regulatory activities of macromolecules based mainly on graphical analysis of their state transition diagrams. The contribution is summarized as follows: (1) Stochastic interpretation of Michaelis-Menten equation is given. (2) Notion of \textit{probability flow} is introduced in relation to detailed balance. (3) A stochastic analogy of \textit{Wegscheider condition} is given in relation to loops in the state transition diagram. (4) A simple graphical method of computing the regulatory activity in terms of ligands' concentrations is obtained for Wegscheider cases.Comment: 20 pages, 13 figure

Finite elements and the discrete variable representation in nonequilibrium Green's function calculations. Atomic and molecular models

In this contribution, we discuss the finite-element discrete variable representation (FE-DVR) of the nonequilibrium Green's function and its implications on the description of strongly inhomogeneous quantum systems. In detail, we show that the complementary features of FEs and the DVR allows for a notably more efficient solution of the two-time Schwinger/Keldysh/Kadanoff-Baym equations compared to a general basis approach. Particularly, the use of the FE-DVR leads to an essential speedup in computing the self-energies. As atomic and molecular examples we consider the He atom and the linear version of H$_3^+$ in one spatial dimension. For these closed-shell models we, in Hartree-Fock and second Born approximation, compute the ground-state properties and compare with the exact findings obtained from the solution of the few-particle time-dependent Schr\"odinger equation.Comment: 12 pages, 3 figures, submitted as proceedings of conference "PNGF IV

Quantum Algorithm for Molecular Properties and Geometry Optimization

It is known that quantum computers, if available, would allow an exponential decrease in the computational cost of quantum simulations. We extend this result to show that the computation of molecular properties (energy derivatives) could also be sped up using quantum computers. We provide a quantum algorithm for the numerical evaluation of molecular properties, whose time cost is a constant multiple of the time needed to compute the molecular energy, regardless of the size of the system. Molecular properties computed with the proposed approach could also be used for the optimization of molecular geometries or other properties. For that purpose, we discuss the benefits of quantum techniques for Newton's method and Householder methods. Finally, global minima for the proposed optimizations can be found using the quantum basin hopper algorithm, which offers an additional quadratic reduction in cost over classical multi-start techniques.Comment: 6 page

Two-qubit Quantum Logic Gate in Molecular Magnets

We proposed a scheme to realize a controlled-NOT quantum logic gate in a dimer of exchange coupled single-molecule magnets, $[\textrm{Mn}_4]_2$. We chosen the ground state and the three low-lying excited states of a dimer in a finite longitudinal magnetic field as the quantum computing bases and introduced a pulsed transverse magnetic field with a special frequency. The pulsed transverse magnetic field induces the transitions between the quantum computing bases so as to realize a controlled-NOT quantum logic gate. The transition rates between the quantum computing bases and between the quantum computing bases and other excited states are evaluated and analyzed.Comment: 7 pages, 2 figure

The Coupled Electronic-Ionic Monte Carlo Simulation Method

Quantum Monte Carlo (QMC) methods such as Variational Monte Carlo, Diffusion Monte Carlo or Path Integral Monte Carlo are the most accurate and general methods for computing total electronic energies. We will review methods we have developed to perform QMC for the electrons coupled to a classical Monte Carlo simulation of the ions. In this method, one estimates the Born-Oppenheimer energy E(Z) where Z represents the ionic degrees of freedom. That estimate of the energy is used in a Metropolis simulation of the ionic degrees of freedom. Important aspects of this method are how to deal with the noise, which QMC method and which trial function to use, how to deal with generalized boundary conditions on the wave function so as to reduce the finite size effects. We discuss some advantages of the CEIMC method concerning how the quantum effects of the ionic degrees of freedom can be included and how the boundary conditions can be integrated over. Using these methods, we have performed simulations of liquid H2 and metallic H on a parallel computer.Comment: 27 pages, 10 figure