Instantaneous Normal Mode Analysis of Supercooled Water

We use the instantaneous normal mode approach to provide a description of the local curvature of the potential energy surface of a model for water. We focus on the region of the phase diagram in which the dynamics may be described by the mode-coupling theory. We find, surprisingly, that the diffusion constant depends mainly on the fraction of directions in configuration space connecting different local minima, supporting the conjecture that the dynamics are controlled by the geometric properties of configuration space. Furthermore, we find an unexpected relation between the number of basins accessed in equilibrium and the connectivity between them.Comment: 5 pages, 4 figure

Instantaneous Normal Mode analysis of liquid HF

We present an Instantaneous Normal Modes analysis of liquid HF aimed to clarify the origin of peculiar dynamical properties which are supposed to stem from the arrangement of molecules in linear hydrogen-bonded network. The present study shows that this approach is an unique tool for the understanding of the spectral features revealed in the analysis of both single molecule and collective quantities. For the system under investigation we demonstrate the relevance of hydrogen-bonding ``stretching'' and fast librational motion in the interpretation of these features.Comment: REVTeX, 7 pages, 5 eps figures included. Minor changes in the text and in a figure. Accepted for publication in Phys. Rev. Let

Quasi-normal mode analysis in BEC acoustic black holes

We perform a quasi-normal mode analysis of black hole configurations in Bose-Einstein condensates (BEC). In this analysis we use the full Bogoliubov dispersion relation, not just the hydrodynamic or geometric approximation. We restrict our attention to one-dimensional flows in BEC with step-like discontinuities. For this case we show that in the hydrodynamic approximation quasi-normal modes do not exist. The full dispersion relation, however, allows the existence of quasi-normal modes. Remarkably, the spectrum of these modes is not discrete but continuous.Comment: 7 pages, 3 figure

Magnetohydrodynamic normal mode analysis of plasma with equilibrium pressure anisotropy

In this work, we generalise linear magnetohydrodynamic (MHD) stability theory to include equilibrium pressure anisotropy in the fluid part of the analysis. A novel 'single-adiabatic' (SA) fluid closure is presented which is complementary to the usual 'double-adiabatic' (CGL) model and has the advantage of naturally reproducing exactly the MHD spectrum in the isotropic limit. As with MHD and CGL, the SA model neglects the anisotropic perturbed pressure and thus loses non-local fast-particle stabilisation present in the kinetic approach. Another interesting aspect of this new approach is that the stabilising terms appear naturally as separate viscous corrections leaving the isotropic SA closure unchanged. After verifying the self-consistency of the SA model, we re-derive the projected linear MHD set of equations required for stability analysis of tokamaks in the MISHKA code. The cylindrical wave equation is derived analytically as done previously in the spectral theory of MHD and clear predictions are made for the modification to fast-magnetosonic and slow ion sound speeds due to equilibrium anisotropy.Comment: 19 pages. This is an author-created, un-copyedited version of an article submitted for publication in Plasma Physics and Controlled Fusion. IOP Publishing Ltd is not responsible for any errors or omissions in this version of the manuscript or any version derived from i

Acoustic wave propagation through a supercooled liquid: A normal mode analysis

The mechanism of acoustic wave propagation in supercooled liquids is not yet fully understood since the vibrational dynamics of supercooled liquids are strongly affected by their amorphous inherent structures. In this paper, the acoustic wave propagation in a supercooled model liquid is studied by using normal mode analysis. Due to the highly disordered inherent structure, a single acoustic wave is decomposed into many normal modes in broad frequency range. This causes the rapid decay of the acoustic wave and results in anomalous wavenumber dependency of the dispersion relation and the rate of attenuation.Comment: 11 pages, 5 figures (color

System for determining the angle of impact of an object on a structure

A method for determining the angle of impact of an object on a thin-walled structure which determines the angle of impact through analysis of the acoustic waves which result when an object impacts a structure is presented. Transducers are placed on and in the surface of the structure which sense the wave caused in the structure by impact. The waves are recorded and saved for analysis. For source motion normal to the surface, the antisymmetric mode has a large amplitude while that of the symmetric mode is very small. As the source angle increases with respect to the surface normal, the symmetric mode amplitude increases while the antisymmetric mode amplitude decreases. Thus, the angle of impact is determined by measuring the relative amplitudes of these two lowest order modes

Normal mode analysis of macromolecular systems with the Mobile Block Hessian method

Until recently, normal mode analysis (NMA) was limited to small proteins, not only because the required energy minimization is a computationally exhausting task, but also because NMA requires the expensive diagonalization of a 3Na 3Na matrix with Na the number of atoms. A series of simplified models has been proposed, in particular the Rotation-Translation Blocks (RTB) method by Tama et al. for the simulation of proteins. It makes use of the concept that a peptide chain or protein can be seen as a subsequent set of rigid components, i.e. the peptide units. A peptide chain is thus divided into rigid blocks with six degrees of freedom each. Recently we developed the Mobile Block Hessian (MBH) method, which in a sense has similar features as the RTB method. The main difference is that MBH was developed to deal with partially optimized systems. The position/orientation of each block is optimized while the internal geometry is kept fixed at a plausible – but not necessarily optimized – geometry. This reduces the computational cost of the energy minimization. Applying the standard NMA on a partially optimized structure however results in spurious imaginary frequencies and unwanted coordinate dependence. The MBH avoids these unphysical effects by taking into account energy gradient corrections. Moreover the number of variables is reduced, which facilitates the diagonalization of the Hessian. In the original implementation of MBH, atoms could only be part of one rigid block. The MBH is now extended to the case where atoms can be part of two or more blocks. Two basic linkages can be realized: (1) blocks connected by one link atom, or (2) by two link atoms, where the latter is referred to as the hinge type connection. In this work we present the MBH concept and illustrate its performance with the crambin protein as an example

Multi-mode bosonic Gaussian channels

A complete analysis of multi-mode bosonic Gaussian channels is proposed. We clarify the structure of unitary dilations of general Gaussian channels involving any number of bosonic modes and present a normal form. The maximum number of auxiliary modes that is needed is identified, including all rank deficient cases, and the specific role of additive classical noise is highlighted. By using this analysis, we derive a canonical matrix form of the noisy evolution of n-mode bosonic Gaussian channels and of their weak complementary counterparts, based on a recent generalization of the normal mode decomposition for non-symmetric or locality constrained situations. It allows us to simplify the weak-degradability classification. Moreover, we investigate the structure of some singular multi-mode channels, like the additive classical noise channel that can be used to decompose a noisy channel in terms of a less noisy one in order to find new sets of maps with zero quantum capacity. Finally, the two-mode case is analyzed in detail. By exploiting the composition rules of two-mode maps and the fact that anti-degradable channels cannot be used to transfer quantum information, we identify sets of two-mode bosonic channels with zero capacity.Comment: 37 pages, 3 figures (minor editing), accepted for publication in New Journal of Physic

Sampling of conformational ensemble for virtual screening using molecular dynamics simulations and normal mode analysis

Aim: Molecular dynamics simulations and normal mode analysis are well-established approaches to generate receptor conformational ensembles (RCEs) for ligand docking and virtual screening. Here, we report new fast molecular dynamics-based and normal mode analysis-based protocols combined with conformational pocket classifications to efficiently generate RCEs. Materials \& methods: We assessed our protocols on two well-characterized protein targets showing local active site flexibility, dihydrofolate reductase and large collective movements, CDK2. The performance of the RCEs was validated by distinguishing known ligands of dihydrofolate reductase and CDK2 among a dataset of diverse chemical decoys. Results \& discussion: Our results show that different simulation protocols can be efficient for generation of RCEs depending on different kind of protein flexibility