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应助: 16 (小学生)
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虫号: 1215917
注册: 2011-02-28
性别: GG
专业: 半导体科学与信息器件

[交流] 几个学习第一性原理动力学的重要网址已有1人参与

1. NIC Series： http://www.fz-juelich.de/nic-series/index.html

(1)2006年 NIC series V31: Computational Nanoscience: do it yourself 是学习第一性原理动力学模拟的起点；
(2) 2000年NIC Series Volume 1: Modern Methods and Algorithms of Quantum Chemistry Proceedings

2.Institute of Physical Chemistry@Univerity of Zurich的资源下载：hhttp://www.pci.uzh.ch/e/download.html

3.CECAM：http://www.cecam.org/
CECAM (Centre Européen de Calcul Atomique et Moléculaire)是一个欧洲的组织，致力于高级计算方法的基础研究和在前沿科技领域的重要问题上的应用。

Aqueous Solvation of IonsLocation : CECAM-ETHZ, Zurich, Switzerland
February 22, 2010 - February 24, 2010

van der Waals forces in DFT, RPA and beyondLocation : CECAM-HQ-EPFL, Lausanne, Switzerland
June 28, 2010 - July 2, 2010

Modeling and Simulation of Water at Interfaces from Ambient to Supercooled Conditions.Location : CECAM-HQ-EPFL, Lausanne, Switzerland
June 29, 2009 - July 1, 2009

Progress in ab initio modelling of biomolecules : towards computational spectroscopy Location : Dipartimento di Fisica Università di Roma
April 2, 2007 - April 4, 2007

Vibrational spectroscopy of small molecules of biological interest in liquid water by Car-Parrinello simulations
Rodolphe Vuilleumier
Ecole Normale Supérieure, Paris

Abstract

Vibrational spectroscopy, infrared or Raman, allows to get structural and dynamical informations about molecules in gaseous and aqueous phases. Ab initio Molecular dynamics simulations was proven to be able to reproduce the experimentally observed spectra in a variety of situations but their interpretation from the simulation is still a challenge. Here, we present an original method for analysing vibrational spectra from ab initio molecular dynamics at finite temperature, that generalizes normal modes to anharmonic systems. With the aid of these effective vibrational modes we can then determine the intensities and the widths of each infrared absorption bands allowing for an interpretation of the predicted signal. This method will be illustrated with the study of the infrared spectrum of N-methylacetamide, a model of the peptide bond, in gas phase and in aqueous solution, and of the vibrational spectrum of small peptides in gas phase.

Hydrogen bonds, cooperativity, and the stability of helical polypeptides: towards a spectroscopic fingerprint
Volker Blum
Fritz Haber Institute, Berlin

Abstract

Hydrogen bonds are the basic stabilizing ingredient in many secondary structure elements of peptides and proteins. In finite polypeptide chains, simple estimates show that the strength of H bonds depends strongly on the length and environment of the peptide: e.g., the energy of a single isolated H bond in a short alpha-helical polypeptide is actually smaller by approximately a factor of two than the same energy for the H bonds of an infinite bulk-like alpha helix with the exact same H bond geometry. This effect is known as cooperativity of H bonds.

We here use the new all-electron / full-potential, numeric atom-centered orbital based code package "FHI-aims" [1] ("Ab Initio Molecular Simulations"

and the PBE generalized-gradient density functional to study the development of H bond cooperativity with chain length n for helical Polyalanine polypeptides
(Ala)_n, for different helix types (3_10, alpha, pi) and termination (neutral or capped by positive alkali ions). For neutrally terminated helices (not experimentally stable in the gas phase), the increase of H bond strength is rather gradual with length. In contrast, an alkali ion termination (stable helices observed in gas phase experiments) stabilizes finite helices both directly, by saturating "dangling" terminating H bonds, and indirectly, by strengthening the remaining H bonds in a short helical chain, compared to the neutral case.

It is a challenge to link these fundamental observations to experiment, by identifying a fingerprint of this cooperativity in the electronic structure of experimentally accessible short gas phase peptides. Besides the ground state electronic structure, this requires the proper description of at least the single (quasi-)particle spectra. We emphasize the importance of quasiparticle effects when comparing the calculated electronic structure with photoemission, and discuss the basic concepts of how many-body perturbation theory in the GW approach can be employed in the numeric atom-centered orbital based framework.

Key References

[1] V. Blum, R. Gehrke, P. Havu, V. Havu, X. Ren, M. Scheffler, The FHI Ab Initio Molecular Simulations (aims) Project, Fritz-Haber-Institut, Berlin (2007).

原网址：http://hi.baidu.com/xijunw/item/295cb9d3b3d040e6b2f777f4

[ 来自科研家族寂寞大虫家族 ]

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