Ab initio molecular dynamics simulations of excited hydrogen halides and methyl halides

Using excited-state ab initio molecular dynamics simulations employing the complete-active-space self-consistent-field approach, we study the mechanism of photodissociation in terms of time evolution of structure, kinetic energy, charges and potential energy for the first excited state of hydrogen halides and methyl halides. Although the hydrogen halides and methyl halides are similar in the photodissociation mechanism, their dynamics are slightly different. The presence of the methyl group causes delay in photodissociation as compared to hydrogen halides.

Buckled nano rod - a two state system: quantum effects on its dynamics

We consider a suspended elastic rod under longitudinal compression. The compression can be used to adjust potential energy for transverse displacements from the harmonic to the double well regime. The two minima in potential energy curve describe two possible buckled states. Using transition state theory (TST) we have calculated the rate of conversion from one state to other. If the strain epsilon = 4 epsilon c the simple TST rate diverges. We suggest a method to correct this divergence for quantum calculations. We also find that zero point energy contributions can be quite large so that single mode calculations can lead to large errors in the rate.

The 5-Methyl Group in Thymine Dynamically Influences the Structure of A-Tracts in DNA at the Local and Global Level

DNA sequences containing a stretch of several A:T basepairs without a 5'-TA-3' step are known as A-tracts and have been the subject of extensive investigation because of their unique structural features such as a narrow minor groove and their crucial role in several biological processes. One of the aspects under investigation has been the influence of the 5-methyl group of thymine on the properties of A-tracts. Detailed molecular dynamics simulation studies of the sequences d(CGCAAAUUUGCG) and d(CGCAAATTTGCG) indicate that the presence of the 5-methyl group in thymine increases the frequency of a narrow minor groove conformation, which could facilitate its specific recognition by proteins, and reduce its susceptibility to cleavage by DNase I. The bias toward a wider minor groove in the absence of the thymine 5-methyl group is a static structural feature. Our results also indicate that the presence of the thymine 5-methyl group is necessary for calibrating the backbone conformation and the basepair and dinucleotide step geometry of the core A-tract as well as the flanking CA/TG and the neighboring GC/GC steps, as observed in free and protein-bound DNA. As a consequence, it also fine-tunes the curvature of the longer DNA fragment in which the A-tract is embedded.

Dynamics of capacitively coupled double quantum dots

We consider a double dot system of equivalent, capacitively coupled semiconducting quantum dots, each coupled to its own lead, in a regime where there are two electrons on the double dot. Employing the numerical renormalization group, we focus here on single-particle dynamics and the zero-bias conductance, considering in particular the rich range of behaviour arising as the interdot coupling is progressively increased through the strong-coupling (SC) phase, from the spin-Kondo regime, across the SU(4) point to the charge-Kondo regime, and then towards and through the quantum phase transition to a charge-ordered ( CO) phase. We first consider the two-self-energy description required to describe the broken symmetry CO phase, and implications thereof for the non-Fermi liquid nature of this phase. Numerical results for single-particle dynamics on all frequency scales are then considered, with particular emphasis on universality and scaling of low-energy dynamics throughout the SC phase. The role of symmetry breaking perturbations is also briefly discussed.

Struggling over subjectivity: A discursive analysis of strategic development in a group

We have seen growing interest in discursive perspectives on strategy. This perspective holds great promise for development of an understanding on how strategy discourse and subjectivity are intertwined. We wish to add to this existing research by outlining a discursive struggle approach to subjectivity. To understand the complex subjectification and empowering/disempowering effects of organizational strategy discourse, this approach focuses on organization-specific discourse mobilizations an various ways of resistance. Drawing on an analysis of the discourses and practices of ‘strategic development’ in an engineering and consulting group we provide an empirical illustration of such struggles over subjectivity. In particular, we report three examples of competing ways of making sense of and giving sense to strategic development, with specific subjectification tendencies. First, we show how corporate management can mobilize and appropriate a specific kind of discourse to attempt to gain control of the organization, which tends to reproduce managerial hegemony, but also trigger discursive and other forms of resistance. Second, we will illustrate how middle managers resist this hegemony by initiating a strategy discourse of their own to create room for manoeuvre in controversial situations. Third, we show how project engineers can distance themselves from managerial-initiated strategy discourses to maintain a viable identity despite all kinds of pressures. Although our examples are case-specific, we believe that similar discursive dynamics also characterize strategizing in other organizations.

Effect of √-irradiation on the structure and dynamics of domains in triglycine selenate

A comparative study of the switching properties of pure and √-irradiated TGSe crystals has been carried out to see the effect of irradiation on the structure and dynamics of domains. The switching behaviour of √-irradiated TGSe has been found to be qualitatively similar to that of unirradiated crystal and this has been interpreted in terms of structural inhibition caused by the formation of radiolysis products as well as the difference between the domain structures of the unirradiated and irradiated samples. Confirmation of this has been obtained by studying the domain patterns using the etch method.

Double time window targeting technique: Real-time DMRG dynamics in the Pariser-Parr-Pople model

We present a generalized adaptive time-dependent density matrix renormalization-group (DMRG) scheme, called the double time window targeting (DTWT) technique, which gives accurate results with nominal computational resources, within reasonable computational time. This procedure originates from the amalgamation of the features of pace keeping DMRG algorithm, first proposed by Luo et al. [Phys. Rev. Lett. 91, 049701 (2003)] and the time-step targeting algorithm by Feiguin and White [Phys. Rev. B 72, 020404 (2005)]. Using the DTWT technique, we study the phenomena of spin-charge separation in conjugated polymers (materials for molecular electronics an spintronics), which have long-range electron-electron interactions and belong to the class of strongly correlated low-dimensional many-body systems. The issue of real-time dynamics within the Pariser-Parr-Pople (PPP) model which includes long-range electron correlations has not been addressed in the literature so far. The present study on PPP chains has revealed that, (i) long-range electron correlations enable both the charge and spin degree of freedom of the electron, to propagate faster in the PPP model compared to Hubbard model, (ii) for standard parameters of the PPP model as applied to conjugated polymers, the charge velocity is almost twice that of the spin velocity, and (iii) the simplistic interpretation of long-range correlations by merely renormalizing the U value of the Hubbard model fails to explain the dynamics of doped holes/electrons in the PPP model.

Modelling the dynamics of a large sea area

Yhteenveto: Laajan merialueen dynamiikan mallintaminen

Effect of √-irradiation on the structure and dynamics of domains in triglycine selenate

A comparative study of the switching properties of pure and √-irradiated TGSe crystals has been carried out to see the effect of irradiation on the structure and dynamics of domains. The switching behaviour of √-irradiated TGSe has been found to be qualitatively similar to that of unirradiated crystal and this has been interpreted in terms of structural inhibition caused by the formation of radiolysis products as well as the difference between the domain structures of the unirradiated and irradiated samples. Confirmation of this has been obtained by studying the domain patterns using the etch method.

Investigations on the melting and bending modulus of polymer grafted bilayers using dissipative particle dynamics

Understanding the influence of polymer grafted bilayers on the physicomechanical properties of lipid membranes is important while developing liposomal based drug delivery systems. The melting characteristics and bending moduli of polymer grafted bilayers are investigated using dissipative particle dynamics simulations as a function of the amount of grafted polymer and lipid tail length. Simulations are carried out using a modified Andersen barostat, whereby the membrane is maintained in a tensionless state. For lipids made up of four to six tail beads, the transition from the low temperature L-beta phase to the L-alpha phase is lowered only above a grafting fraction of G(f)=0.12 for polymers made up of 20 beads. Below G(f)=0.12 small changes are observed only for the HT4 bilayer. The bending modulus of the bilayers is obtained as a function of G(f) from a Fourier analysis of the height fluctuations. Using the theory developed by Marsh Biochim. Biophys. Acta 1615, 33 (2003)] for polymer grafted membranes, the contributions to the bending modulus due to changes arising from the grafted polymer and bilayer thinning are partitioned. The contributions to the changes in kappa from bilayer thinning were found to lie within 11% for the lipids with four to six tail beads, increasing to 15% for the lipids containing nine tail beads. The changes in the area stretch modulus were also assessed and were found to have a small influence on the overall contribution from membrane thinning. The increase in the area per head group of the lipids was found to be consistent with the scalings predicted by self-consistent mean field results. (C) 2010 American Institute of Physics.

1H NMR study of molecular dynamics and phase transition in (NH4)2ZnBr4

The proton second moment (M2) and spin-lattice relaxation time (T1) have been measured in (NH4)2ZnBr4 in the range 77-300 K. The room-temperature spectrum shows a structure which disappears around 243 K. The signal is strong and narrow even at 77 K. Proton T1 shows a maximum at 263 K, caused by spin rotation interaction and decreases with decreasing temperature till 235 K, where it shows a sudden increase. Below 235 K, again it decreases and shows a slope change around 216.5 K (reported Tc). From 216.5 K, T1 decreases continuously without exhibiting any minimum down to 77 K. The narrow line at 77 K, and absence of a T1 minimum down to 77 K indicate the possibility of quantum mechanical tunnelling in this system. Motional parameters such as activation energy and pre-exponential factor have been evaluated for the reorientational motion of the NH+4 ion.

E. C. G. Sudarshan and Symmetry in Classical Dynamics, Optics and Quantum Mechanics

We review work initiated and inspired by Sudarshan in relativistic dynamics, beam optics, partial coherence theory, Wigner distribution methods, multimode quantum optical squeezing, and geometric phases. The 1963 No Interaction Theorem using Dirac's instant form and particle World Line Conditions is recalled. Later attempts to overcome this result exploiting constrained Hamiltonian theory, reformulation of the World Line Conditions and extending Dirac's formalism, are reviewed. Dirac's front form leads to a formulation of Fourier Optics for the Maxwell field, determining the actions of First Order Systems (corresponding to matrices of Sp(2,R) and Sp(4,R)) on polarization in a consistent manner. These groups also help characterize properties and propagation of partially coherent Gaussian Schell Model beams, leading to invariant quality parameters and the new Twist phase. The higher dimensional groups Sp(2n,R) appear in the theory of Wigner distributions and in quantum optics. Elegant criteria for a Gaussian phase space function to be a Wigner distribution, expressions for multimode uncertainty principles and squeezing are described. In geometric phase theory we highlight the use of invariance properties that lead to a kinematical formulation and the important role of Bargmann invariants. Special features of these phases arising from unitary Lie group representations, and a new formulation based on the idea of Null Phase Curves, are presented.

Crystal structures, dynamics and functional implications of molybdenum-cofactor biosynthesis protein MogA from two thermophilic organisms

Molybdenum-cofactor (Moco) biosynthesis is an evolutionarily conserved pathway in almost all kingdoms of life, including humans. Two proteins, MogA and MoeA, catalyze the last step of this pathway in bacteria, whereas a single two-domain protein carries out catalysis in eukaryotes. Here, three crystal structures of the Moco-biosynthesis protein MogA from the two thermophilic organisms Thermus thermophilus (TtMogA; 1.64 angstrom resolution, space group P2(1)) and Aquifex aeolicus (AaMogA; 1.70 angstrom resolution, space group P2(1) and 1.90 angstrom resolution, space group P1) have been determined. The functional roles and the residues involved in oligomerization of the protein molecules have been identified based on a comparative analysis of these structures with those of homologous proteins. Furthermore, functional roles have been proposed for the N- and C-terminal residues. In addition, a possible protein-protein complex of MogA and MoeA has been proposed and the residues involved in protein-protein interactions are discussed. Several invariant water molecules and those present at the subunit interfaces have been identified and their possible structural and/or functional roles are described in brief. In addition, molecular-dynamics and docking studies with several small molecules (including the substrate and the product) have been carried out in order to estimate their binding affinities towards AaMogA and TtMogA. The results obtained are further compared with those obtained for homologous eukaryotic proteins.