Parametrically driven dark solitons

We show that unlike the bright solitons, the parametrically driven kinks are immune from instabilities for all dampings and forcing amplitudes; they can also form stable bound states. In the undamped case, the two types of stable kinks and their complexes can travel with nonzero velocities.     

A DFT investigation of anthocyanidins

A theoretical analysis of anthocyanidins, a class of natural plant pigments, has been conducted using density functional theory at the B3LYP/6-31G(d) level. It is found that these compounds are non-planar, with the 2-phenyl ring twisted relative to the benzopyrylium rings. TD-DFT calculations reveal a first excited state dominated by two orbital transitions, including the HOMO–LUMO transition. From a comparison of these molecular orbitals with those of related compounds, and from the known chemistry of these compounds, it is suggested that anthocyanidins should be regarded as natural, stable carbocations.     

Canonical Proper-Time Formulation of Relativistic Particle Dynamics. II

Our purpose in this paper is to provide theframework for a generalization of classical mechanicsand electrodynamics, including Maxwell's theory, whichis simple, technically correct, and requires noadditional work for the quantum case. We first show thatthere are two other definitions of proper-time, eachhaving equal status with the Minkowski definition. Weuse the first definition, called the proper-velocity definition, to construct a transformationtheory which fixes the proper-time of a given physicalsystem for all observers. This leads to a new invariancegroup and a generalization of Maxwell's equations left covariant under the action of this group.The second definition, called the canonical variablesdefinition, has the unique property that it isindependent of the number of particles. This definition leads to a general theory of directlyinteracting relativistic particles. We obtain theLorentz force for one particle (using its proper-time),and the Lorentz force for the total system (using theglobal proper-time). Use of the global proper-time tocompute the force on one particle gives the Lorentzforce plus a dissipative term corresponding to thereaction of this particle back on the cause of itsacceleration (Newton's third law). The wave equation derivedfrom Maxwell's equations has an additional term, firstorder in the proper-time. This term arisesinstantaneously with acceleration. This shows explicitly that the longsought origin of radiationreaction is inertial resistance to changes in particlemotion. The field equations carry intrinsic informationabout the velocity and acceleration of the particles in the system. It follows that our theory isnot invariant under time reversal, so that the existenceof radiation introduces an arrow for the (proper-time ofthe) system.     

Temperature dependent deuterium quadrupole coupling constants of short hydrogen bonds

Very short hydrogen bonds universally show large positive dependences of the deuterium NMR quadrupolar coupling constant with temperature. We present temperature dependent NMR data for eight such systems, with OO distances of between 238 and 250 pm, and show we can model the temperature dependences by density functional methods, as long as proper attention is paid to intermolecular effects and intermode couplings.     

Smooth curve interpolation

In a recent paper [1] a method was presented for smooth curve interpolation by means of minimising the energy of an idealised elastic beam constrained to pass through given data points. This method of obtaining the curve required an enormous amount of computation, since it involved the repeated solution of a fourth order differential equation and the minimisation of a function of many variables, the number of variables being equal to the number of data points. In this paper a much simpler method is presented for finding the minimum energy curve in which the minimisation procedure is eliminated. An ALGOL procedure to perform the curve fit is supplied.     

Density functional theory and atoms-in-molecules investigation of intramolecular hydrogen bonding in derivatives of malonaldehyde and implications for resonance-assisted hydrogen bonding

A density functional theory (DFT) and atoms-in-molecules (AIM) analysis has been applied to the intramolecular hydrogen bonding in the enol conformers of malonaldehyde and its fluoro-, chloro-, cyano-, and nitro-substituted derivatives. With the B3LYP/6-311++G(2d,p) method, good agreement between the DFT geometries and published experimental structures has been found. The donor-acceptor distance was also varied in a series of constrained optimizations in order to determine if energetic, structural, and topological trends associated with intermolecular hydrogen bonding remain valid in the intramolecular case. At very short donor-acceptor distances (<2.24 A), the hydrogen is symmetrically located between donor and acceptor; at distances longer than this, the hydrogen bonding is no longer symmetric. The AIM methodology has been applied to explore the topology of the electron density in the intramolecular hydrogen bonds of the chosen model systems. Most AIM properties for intramolecular hydrogen bond distances longer than 2.24 A show smooth trends, consistent with intermolecular hydrogen bonds. Integrated AIM properties have also been used to explore the phenomenon of resonance-assisted hydrogen bonding (RAHB). It is shown that as the donor-acceptor distance is varied, pi-electron density is redistributed among the carbon atoms in the intramolecular hydrogen bond ring; however, contrary to prior studies, the integrated atomic charges on the donor-acceptor atoms were found to be insensitive to variation of hydrogen-bonding distance.     

Chemical Perturbation of Oncogenic Protein Folding: from the Prediction of Locally Unstable Structures to the Design of Disruptors of Hsp90–Client Interactions

Protein folding quality control in cells requires the activity of a class of proteins known as molecular chaperones. Heat shock protein-90 (Hsp90), a multidomain ATP driven molecular machine, is a prime representative of this family of proteins. Interactions between Hsp90, its co-chaperones, and client proteins have been shown to be important in facilitating the correct folding and activation of clients. Hsp90 levels and functions are elevated in tumor cells. Here, we computationally predict the regions on the native structures of clients c-Abl, c-Src, Cdk4, B-Raf and Glucocorticoid Receptor, that have the highest probability of undergoing local unfolding, despite being ordered in their native structures. Such regions represent potential ideal interaction points with the Hsp90-system. We synthesize mimics spanning these regions and confirm their interaction with partners of the Hsp90 complex (Hsp90, Cdc37 and Aha1) by Nuclear Magnetic Resonance (NMR). Designed mimics selectively disrupt the association of their respective clients with the Hsp90 machinery, leaving unrelated clients unperturbed and causing apoptosis in cancer cells. Overall, selective targeting of Hsp90 protein–protein interactions is achieved without causing indiscriminate degradation of all clients, setting the stage for the development of therapeutics based on specific chaperone:client perturbation.