Correlations in Systems of Complex Directed Macromolecules

An ensemble of directed macromolecules on a lattice is considered, where the constituting molecules are chosen as a random sequence of N different types. The same type of molecules experiences a hard-core (exclusion) interaction. We study the robustness of the macromolecules with respect to breaking and substituting individual molecules, using a 1/N expansion. The properties depend strongly on the density of macromolecules. In particular, the macromolecules are robust against breaking and substituting at high densities.Comment: 9 pages, 4 figure

Mechanically bonded macromolecules

Mechanically bonded macromolecules constitute a class of challenging synthetic targets in polymer science. The controllable intramolecular motions of mechanical bonds, in combination with the processability and useful physical and mechanical properties of macromolecules, ultimately ensure their potential for applications in materials science, nanotechnology and medicine. This tutorial review describes the syntheses and properties of a library of diverse mechanically bonded macromolecules, which covers (i) main-chain, side-chain, bridged, and pendant oligo/polycatenanes, (ii) main-chain oligo/polyrotaxanes, (iii) poly[c2]daisy chains, and finally (iv) mechanically interlocked dendrimers. A variety of highly efficient synthetic protocols—including template-directed assembly, step-growth polymerisation, quantitative conjugation, etc.—were employed in the construction of these mechanically interlocked architectures. Some of these structures, i.e., side-chain polycatenanes and poly[c2]daisy chains, undergo controllable molecular switching in a manner similar to their small molecular counterparts. The challenges posed by the syntheses of polycatenanes and polyrotaxanes with high molecular weights are contemplated

Nanotrapping and the thermodynamics of optical tweezers

Particles that can be trapped in optical tweezers range from tens of microns down to tens of nanometres in size. Interestingly, this size range includes large macromolecules. We show experimentally, in agreement with theoretical expectations, that optical tweezers can be used to manipulate single molecules of polyethylene oxide suspended in water. The trapped molecules accumulate without aggregating, so this provides optical control of the concentration of macromolecules in solution. Apart from possible applications such as the micromanipulation of nanoparticles, nanoassembly, microchemistry, and the study of biological macromolecules, our results also provide insight into the thermodynamics of optical tweezers.Comment: 5 pages, 3 figures, presented at 17th AIP Congress, Brisbane, 200

Force steps during viral DNA packaging ?

Biophysicists and structural biologists increasingly acknowledge the role played by the mechanical properties of macromolecules as a critical element in many biological processes. This change has been brought about, in part, by the advent of single molecule biophysics techniques that have made it possible to exert piconewton forces on key macromolecules and observe their deformations at nanometer length scales, as well as to observe the mechanical action of macromolecules such as molecular motors. This has opened up immense possibilities for a new generation of mechanical investigations that will respond to such measurements in an attempt to develop a coherent theory for the mechanical behavior of macromolecules under conditions where thermal and chemical effects are on an equal footing with deterministic forces. This paper presents an application of the principles of mechanics to the problem of DNA packaging, one of the key events in the life cycle of bacterial viruses with special reference to the nature of the internal forces that are built up during the DNA packaging process.Comment: 18 pages, 7 figures, To appear in the Journal of Mechanics and Physics of Solid

3 decades research on mocromolecular differential scanning calorimetry in Biophysical chemistry lab

Biological activity of protein depends on their proper structure and stability. Study on macromolecular stability has attracted many scientists. There are many methods to drive the thermodynamic parameters of macromolecules. Differential Scanning Calorimetry (DSC) is unique and powerful tool which directly measures the thermodynamic parameters of macromolecules. Ordinary, thermodynamic parameters are driven based on assumption that there is equilibrium between folded and unfolded state of macromolecules. It is well known that this hypothesis is not valid for most of bio-macromolecules and their unfolding is an irreversible process. From this point of view protein unfolding is kinetically controlled process. For irreversible macromolecules, DSC thermograms are obtained at different scanning rates and protein concentrations. Then curves are analyzed by fitting the data to theoretical equations for the dependence of the excess heat capacity on temperature. In our lecture will have an overview on 3 decades of macromolecular calorimetry in Biophysical Chemistry Lab of Ibb

Nonlinear screening of charged macromolecules

We present several aspects of the screening of charged macromolecules in an electrolyte. After a review of the basic mean field approach, based on the linear Debye-Huckel theory, we consider the case of highly charged macromolecules, where the linear approximation breaks down and the system is described by full nonlinear Poisson-Boltzmann equation. Some analytical results for this nonlinear equation give some interesting insight on physical phenomena like the charge renormalization and the Manning counterion condensation

Contact Kinetics in Fractal Macromolecules

We consider the kinetics of first contact between two monomers of the same macromolecule. Relying on a fractal description of the macromolecule, we develop an analytical method to compute the Mean First Contact Time (MFCT) for various molecular sizes. In our theoretical description, the non-Markovian feature of monomer motion, arising from the interactions with the other monomers, is captured by accounting for the non-equilibrium conformations of the macromolecule at the very instant of first contact. This analysis reveals a simple scaling relation for the MFCT between two monomers, which involves only their equilibrium distance and the spectral dimension of the macromolecule, independently of its microscopic details. Our theoretical predictions are in excellent agreement with numerical stochastic simulations

Dynamics of polydisperse irreversible adsorption: a pharmacological example

Many drug delivery systems suffer from undesirable interactions with the host immune system. It has been experimentally established that covalent attachment (irreversible adsorption) of suitable macromolecules to the surface of the drug carrier can reduce such undesirable interactions. A fundamental understanding of the adsorption process is still lacking. In this paper, the classical random irreversible adsorption model is generalized to capture certain essential processes involved in pharmacological applications, allowing for macromolecules of different sizes, partial overlapping of the tails of macromolecules, and the influence of reactions with the solvent on the adsorption process. Working in one dimension, an integro-differential evolution equation for the adsorption process is derived, and the asymptotic behavior of the surface area covered and the number of molecules attached to the surface are studied. Finally, equation-free dynamic renormalization tools are applied to study the asymptotically self-similar behavior of the adsorption statistics