Temperature dependent free energy surface of polymer folding from equilibrium and quench studies

Langevin dynamics simulation studies have been employed to calculate the temperature dependent free energy surface and folding characteristics of a 500 monomer long linear alkane (polyethylene) chain with a realistic interaction potential. Both equilibrium and temperature quench simulation studies have been carried out. Using the shape anisotropy parameter (S) of the folded molecule as the order parameter, we find a weakly first order phase transition between the high-temperature molten globule and low-temperature rodlike crystalline states separated by a small barrier of the order of k(B)T. Near the melting temperature (580 K), we observe an intriguing intermittent fluctuation with pronounced ``1/f noise characteristics'' between these two states with large difference in shape and structure. We have also studied the possibilities of different pathways of folding to states much below the melting point. At 300 K starting from the all-trans linear configuration, the chain folds stepwise into a very regular fourfold crystallite with very high shape anisotropy. Whereas, when quenched from a high temperature (900 K) random coil regime, we identify a two step transition from the random coiled state to a molten globulelike state and, further, to a anisotropic rodlike state. The trajectory reveals an interesting coupling between the two order parameters, namely, radius of gyration (R-g) and the shape anisotropy parameter (S). The rodlike final state of the quench trajectory is characterized by lower shape anisotropy parameter and significantly larger number of gauche defects as compared to the final state obtained through equilibrium simulation starting from all-trans linear chain. The quench study shows indication of a nucleationlike pathway from the molten globule to the rodlike state involving an underlying rugged energy landscape. (C) 2010 American Institute of Physics. doi:10.1063/1.3509398]

Out-of-equilibrium microrheology using optical tweezers to probe directional viscoelastic properties under shear

Many wormlike micellar systems exhibit appreciable shear thinning due to shear-induced alignment. As the micelles get aligned introducing directionality in the system, the viscoelastic properties are no longer expected to be isotropic. An optical-tweezers-based active microrheology technique enables us to probe the out-of-equilibrium rheological properties of a wormlike micellar system simultaneously along two orthogonal directions-parallel to the applied shear, as well as perpendicular to it. While the displacements of a trapped bead in response to active drag force carry signature of conventional shear thinning, its spontaneous position fluctuations along the perpendicular direction manifest an orthogonal shear thickening, an effect hitherto unobserved. Copyright (C) EPLA, 2010

Squeezed states, photon-number distributions, and U(l) invariance

We study the photon-number distribution in squeezed states of a single-mode radiation field. A U(l)-invariant squeezing criterion is compared and contrasted with a more restrictive criterion, with the help of suggestive geometric representations. The U(l) invariance of the photon-number distribution in a squeezed coherent state, with arbitrary complex squeeze and displacement parameters, is explicitly demonstrated. The behavior of the photon-number distribution for a representative value of the displacement and various values of the squeeze parameter is numerically investigated. A new kind of giant oscillation riding as an envelope over more rapid oscillations in this distribution is demonstrated.

Lattice embedding and equilibrium geometry of metal-halogen chains in the two-band extended Hubbard model

Two-band extended Hubbard model studies show that the shift in optical gap of the metal-halogen (MX) chain upon embedding in a crystalline environment depends upon alternation in the site-diagonal electron-lattice interaction parameter (epsilon(M)) and the strength of electron-electron interactions at the metal site (U(M)). The equilibrium geometry studies on isolated chains show that the MX chains tend to distort for alternating epsilon(M) and small U(M) values.

Glass Transition in the Density Functional Theory of Freezing

A mean-field description of the glass transition in the hard-sphere system is obtained by numerically locating "glassy" minima of a model free-energy functional. These minima, characterized by inhomogeneous but aperiodic density distributions, appear as the average density is increased above the value at which equilibrium crystallization takes place. Investigations of the density distribution and local bond-orientational order at these minima yield results similar to those obtained from simulations.

Injection cooling of blunt bodies flying at high Mach numbers

A study of transpiration cooling of blunt bodies such as a hemicylinder is made by solving Navier-Stokes equations. An upwind, implicit time-marching code is developed for this purpose. The study is conducted for both perfect-gas and real-gas (chemical equilibrium) flows. Investigations are carried out for a special wall condition that is referred to as no heat flow into the wall condition. The effects of air injection on wall temperature are analyzed. Analyses are carried out for Mach numbers ranging between 6-10 and Reynolds numbers ranging between 10(6)-10(7). Studies are made for spatially constant as well as spatially varying mass injection rate distributions, White cold air injection reduces the wall temperature substantially, transpiration cooling is relatively less effective when the gas is in chemical equilibrium.

Lamination-dependent shear deformation models for bending of angle-ply laminated plates

Lamination-dependent shear corrective terms in the analysis of bending of laminated plates are derived from a priori assumed linear thicknesswise distributions for gradients of transverse shear stresses by using CLPT inplane stresses in the two in-plane equilibrium equations of elasticity in each ply. In the development of a general model for angle-ply laminated plates, special cases like cylindrical bending of laminates in either direction, symmetric laminates, cross-ply laminates, antisymmetric angle-ply laminates, homogeneous plates are taken into consideration. Adding these corrective terms to the assumed displacements in (i) Classical Laminate Plate Theory (CLPT) and (ii) Classical Laminate Shear Deformation Theory (CLSDT), two new refined lamination-dependent shear deformation models are developed. Closed form solutions from these models are obtained for antisymmetric angle-ply laminates under sinusoidal load for a type of simply supported boundary conditions. Results obtained from the present models and also from Ren's model (1987) are compared with each other.

Lamination-dependent shear deformation models for cylindrical bending of angle-ply laminates

Lamination-dependent shear corrective terms in the analysis of flexure of laminates are derived from a priori assumed linear thicknesswise distributions for gradients of transverse shear stresses and using them in the two in-plane equilibrium equations of elasticity in each ply. Adding these corrective terms to (i) Classical Laminate Plate Theory (CLPT) displacements and (ii) Classical Laminate Shear Deformation Theory (CLSDT) displacements, four new refined lamination-dependent shear deformation models for angle-ply laminates are developed. Performance of these models is evaluated by comparing the results from these models with those from exact elasticity solutions for antisymmetric 2-ply laminates and for 4-ply [15/-15](s) laminates. In general, the model with shear corrective terms based on CLPT and added to CLSDT displacements is sufficient and predicts good estimates, both qualitatively and quantitatively, for all displacements and stresses.

Spin distributions in antiferromagnetically coupled Mn2+Cu2+ systems: from the pair to the infinite chain

Probably the most informative description of the ground slate of a magnetic molecular species is provided by the spin density map. Such a map may be experimentally obtained from polarized neutron diffraction (PND) data or theoretically calculated using quantum chemical approaches. Density functional theory (DFT) methods have been proved to be well-adapted for this. Spin distributions in one-dimensional compounds may also be computed using the density matrix renormalization group (DMRG) formalism. These three approaches, PND, DFT, and DMRG, have been utilized to obtain new insights on the ground state of two antiferromagnetically coupled Mn2+Cu2+ compounds, namely [Mn(Me-6-[14]ane-N-4)Cu(oxpn)](CF3SO3)(2) and MnCu(pba)(H2O)(3) . 2H(2)O, with Me-6-[14]ane-N-4 = (+/-)-5,7,7,12,14,14-hexamethyl-1,4,8,11-tetraazacyclotetradecane, oxpn = N,N'-bis(3-aminopropyl)oxamido and pba = 1,3-propylenebis(oxamato). Three problems in particular have been investigated: the spin distribution in the mononuclear precursors [Cu(oxpn)] and [Cu(pba)](2-), the spin density maps in the two Mn2+Cu2+ compounds, and the evolution of the spin distributions on the Mn2+ and Cu2+ sites when passing from a pair to a one-dimensional ferrimagnet.

The Equations of Equilibrium in Orthogonal Curvilinear Reference Coordinates

Analytical solutions to problems in finite elasticity are most often derived using the semi-inverse approach along with the spatial form of the equations of motion involving the Cauchy stress tensor. This procedure is somewhat indirect since the spatial equations involve derivatives with respect to spatial coordinates while the unknown functions are in terms of material coordinates, thus necessitating the use of the chain rule. In this classroom note, we derive compact expressions for the components of the divergence, with respect to orthogonal material coordinates, of the first Piola-Kirchhoff stress tensor. The spatial coordinate system is also assumed to be an orthogonal curvilinear one, although, not necessarily of the same type as the material coordinate system. We show by means of some example applications how analytical solutions can be derived more directly using the derived results.