158 research outputs found
A mathematical and computational review of Hartree-Fock SCF methods in Quantum Chemistry
We present here a review of the fundamental topics of Hartree-Fock theory in
Quantum Chemistry. From the molecular Hamiltonian, using and discussing the
Born-Oppenheimer approximation, we arrive to the Hartree and Hartree-Fock
equations for the electronic problem. Special emphasis is placed in the most
relevant mathematical aspects of the theoretical derivation of the final
equations, as well as in the results regarding the existence and uniqueness of
their solutions. All Hartree-Fock versions with different spin restrictions are
systematically extracted from the general case, thus providing a unifying
framework. Then, the discretization of the one-electron orbitals space is
reviewed and the Roothaan-Hall formalism introduced. This leads to a exposition
of the basic underlying concepts related to the construction and selection of
Gaussian basis sets, focusing in algorithmic efficiency issues. Finally, we
close the review with a section in which the most relevant modern developments
(specially those related to the design of linear-scaling methods) are commented
and linked to the issues discussed. The whole work is intentionally
introductory and rather self-contained, so that it may be useful for non
experts that aim to use quantum chemical methods in interdisciplinary
applications. Moreover, much material that is found scattered in the literature
has been put together here to facilitate comprehension and to serve as a handy
reference.Comment: 64 pages, 3 figures, tMPH2e.cls style file, doublesp, mathbbol and
subeqn package
Second law, entropy production, and reversibility in thermodynamics of information
We present a pedagogical review of the fundamental concepts in thermodynamics
of information, by focusing on the second law of thermodynamics and the entropy
production. Especially, we discuss the relationship among thermodynamic
reversibility, logical reversibility, and heat emission in the context of the
Landauer principle and clarify that these three concepts are fundamentally
distinct to each other. We also discuss thermodynamics of measurement and
feedback control by Maxwell's demon. We clarify that the demon and the second
law are indeed consistent in the measurement and the feedback processes
individually, by including the mutual information to the entropy production.Comment: 43 pages, 10 figures. As a chapter of: G. Snider et al. (eds.),
"Energy Limits in Computation: A Review of Landauer's Principle, Theory and
Experiments
Epidemiology of gastrointestinal symptoms in young and middle-aged Swiss adults: prevalences and comorbidities in a longitudinal population cohort over 28 years
Precise Regulation of Gene Expression Dynamics Favors Complex Promoter Architectures
Promoters process signals through recruitment of transcription factors and RNA polymerase, and dynamic changes in promoter activity constitute a major noise source in gene expression. However, it is barely understood how complex promoter architectures determine key features of promoter dynamics. Here, we employ prototypical promoters of yeast ribosomal protein genes as well as simplified versions thereof to analyze the relations among promoter design, complexity, and function. These promoters combine the action of a general regulatory factor with that of specific transcription factors, a common motif of many eukaryotic promoters. By comprehensively analyzing stationary and dynamic promoter properties, this model-based approach enables us to pinpoint the structural characteristics underlying the observed behavior. Functional tradeoffs impose constraints on the promoter architecture of ribosomal protein genes. We find that a stable scaffold in the natural design results in low transcriptional noise and strong co-regulation of target genes in the presence of gene silencing. This configuration also exhibits superior shut-off properties, and it can serve as a tunable switch in living cells. Model validation with independent experimental data suggests that the models are sufficiently realistic. When combined, our results offer a mechanistic explanation for why specific factors are associated with low protein noise in vivo. Many of these findings hold for a broad range of model parameters and likely apply to other eukaryotic promoters of similar structure
The one dimensional Kondo lattice model at partial band filling
The Kondo lattice model introduced in 1977 describes a lattice of localized
magnetic moments interacting with a sea of conduction electrons. It is one of
the most important canonical models in the study of a class of rare earth
compounds, called heavy fermion systems, and as such has been studied
intensively by a wide variety of techniques for more than a quarter of a
century. This review focuses on the one dimensional case at partial band
filling, in which the number of conduction electrons is less than the number of
localized moments. The theoretical understanding, based on the bosonized
solution, of the conventional Kondo lattice model is presented in great detail.
This review divides naturally into two parts, the first relating to the
description of the formalism, and the second to its application. After an
all-inclusive description of the bosonization technique, the bosonized form of
the Kondo lattice hamiltonian is constructed in detail. Next the
double-exchange ordering, Kondo singlet formation, the RKKY interaction and
spin polaron formation are described comprehensively. An in-depth analysis of
the phase diagram follows, with special emphasis on the destruction of the
ferromagnetic phase by spin-flip disorder scattering, and of recent numerical
results. The results are shown to hold for both antiferromagnetic and
ferromagnetic Kondo lattice. The general exposition is pedagogic in tone.Comment: Review, 258 pages, 19 figure
Adolescent Brain Development and the Risk for Alcohol and Other Drug Problems
Dynamic changes in neurochemistry, fiber architecture, and tissue composition occur in the adolescent brain. The course of these maturational processes is being charted with greater specificity, owing to advances in neuroimaging and indicate grey matter volume reductions and protracted development of white matter in regions known to support complex cognition and behavior. Though fronto-subcortical circuitry development is notable during adolescence, asynchronous maturation of prefrontal and limbic systems may render youth more vulnerable to risky behaviors such as substance use. Indeed, binge-pattern alcohol consumption and comorbid marijuana use are common among adolescents, and are associated with neural consequences. This review summarizes the unique characteristics of adolescent brain development, particularly aspects that predispose individuals to reward seeking and risky choices during this phase of life, and discusses the influence of substance use on neuromaturation. Together, findings in this arena underscore the importance of refined research and programming efforts in adolescent health and interventional needs
Organic Cation Transporter 1 (OCT1) mRNA expression in hepatocellular carcinoma as a biomarker for sorafenib treatment
Effective and safe proton pump inhibitor therapy in acid-related diseases – A position paper addressing benefits and potential harms of acid suppression
- …