Benchmark of dynamic electron correlation models for seniority-zero wavefunctions and their application to thermochemistry

Wavefunctions restricted to electron-pair states are promising models to describe static/nondynamic electron correlation effects encountered, for instance, in bond-dissociation processes and transition-metal and actinide chemistry. To reach spectroscopic accuracy, however, the missing dynamic electron correlation effects that cannot be described by electron-pair states need to be included \textit{a posteriori}. In this article, we extend the previously presented perturbation theory models with an Antisymmetric Product of 1-reference orbital Geminal (AP1roG) reference function that allow us to describe both static/nondynamic and dynamic electron correlation effects. Specifically, our perturbation theory models combine a diagonal and off-diagonal zero-order Hamiltonian, a single-reference and multi-reference dual state, and different excitation operators used to construct the projection manifold. We benchmark all proposed models as well as an \textit{a posteriori} linearized coupled cluster correction on top of AP1roG against CR-CCSD(T) reference data for reaction energies of several closed-shell molecules that are extrapolated to the basis set limit. Moreover, we test the performance of our new methods for multiple bond breaking processes in the N$_2$, C$_2$, and BN dimers against MRCI-SD and MRCI-SD+Q reference data. Our numerical results indicate that the best performance is obtained from a linearized coupled cluster correction as well as second-order perturbation theory corrections employing a diagonal and off-diagonal zero-order Hamiltonian and a single-determinant dual state. These dynamic corrections on top of AP1roG allow us to reliably model molecular systems dominated by static/nondynamic as well as dynamic electron correlation.Comment: 15 pages, 2 figure

Elucidation of molecular kinetic schemes from macroscopic traces using system identification

Overall cellular responses to biologically-relevant stimuli are mediated by networks of simpler lower-level processes. Although information about some of these processes can now be obtained by visualizing and recording events at the molecular level, this is still possible only in especially favorable cases. Therefore the development of methods to extract the dynamics and relationships between the different lower-level (microscopic) processes from the overall (macroscopic) response remains a crucial challenge in the understanding of many aspects of physiology. Here we have devised a hybrid computational-analytical method to accomplish this task, the SYStems-based MOLecular kinetic scheme Extractor (SYSMOLE). SYSMOLE utilizes system-identification input-output analysis to obtain a transfer function between the stimulus and the overall cellular response in the Laplace-transformed domain. It then derives a Markov-chain state molecular kinetic scheme uniquely associated with the transfer function by means of a classification procedure and an analytical step that imposes general biological constraints. We first tested SYSMOLE with synthetic data and evaluated its performance in terms of its rate of convergence to the correct molecular kinetic scheme and its robustness to noise. We then examined its performance on real experimental traces by analyzing macroscopic calcium-current traces elicited by membrane depolarization. SYSMOLE derived the correct, previously known molecular kinetic scheme describing the activation and inactivation of the underlying calcium channels and correctly identified the accepted mechanism of action of nifedipine, a calcium-channel blocker clinically used in patients with cardiovascular disease. Finally, we applied SYSMOLE to study the pharmacology of a new class of glutamate antipsychotic drugs and their crosstalk mechanism through a heteromeric complex of G protein-coupled receptors. Our results indicate that our methodology can be successfully applied to accurately derive molecular kinetic schemes from experimental macroscopic traces, and we anticipate that it may be useful in the study of a wide variety of biological systems

The canonical effect in statistical models for relativistic heavy ion collisions

Enforcing exact conservation laws instead of average ones in statistical thermal models for relativistic heavy ion reactions gives raise to so called canonical effect, which can be used to explain some enhancement effects when going from elementary (e.g. pp) or small (pA) systems towards large AA systems. We review the recently developed method for computation of canonical statistical thermodynamics, and give an insight when this is needed in analysis of experimental data.Comment: 4 pages, 3 figures. Talk given in Strangeness in Quark Matter, Frankfurt am Main 2001. Submitted to J. Phys. G: Nucl. Part. Phy

Theories, models, simulations: a computational challenge

In this talk I would like to illustrate with examples taken from Quantum Field Theory and Biophysics how an intelligent exploitation of the unprecedented power of today's computers could led not only to the solution of pivotal problems in the theory of Strong Interactions, but also to the emergence of new lines of interdisciplinary research, while at the same time pushing the limits of modeling to the realm of living systems.Comment: 19 pages, 1 figure, conference pape