Theory of polymer breaking under tension

We consider the breaking of a polymer molecule which is fixed at one end and is acted upon by a force at the other. The polymer is assumed to be a linear chain joined together by bonds which satisfy the Morse potential. The applied force is found to modify the Morse potential so that the minimum becomes metastable. Breaking is just the decay of this metastable bond, by causing it to go over the barrier. Increasing the force causes the potential to become more and more distorted and eventually leads to the disappearance of the barrier. The limiting force at which the barrier disappears is D(e)a/2,D-e with a the parameters characterizing the Morse potential. The rate of breaking is first calculated using multidimensional quantum transition state theory. We use the harmonic approximation to account for vibrations of all the units. It includes tunneling contributions to the rate, but is valid only above a certain critical temperature. It is possible to get an analytical expression for the rate of breaking. We have calculated the rate of breaking for a model, which mimics polyethylene. First we calculate the rate of breaking of a single bond, without worrying about the other bonds. Inclusion of other bonds under the harmonic approximation is found to lower this rate by at the most one order of magnitude. Quantum effects are found to increase the rate of breaking and are significant only at temperatures less than 150 K. At 300 K, the calculations predict a bond in polyethylene to have a lifetime of only seconds at a force which is only half the limiting force. Calculations were also done using the Lennard-Jones potential. The results for Lennard-Jones and Morse potentials were rather different, due to the different long-range behaviors of the two potentials. A calculation including friction was carried out, at the classical level, by assuming that each atom of the chain is coupled to its own collection of harmonic oscillators. Comparison of the results with the simulations of Oliveira and Taylor [J. Chem. Phys. 101, 10 118 (1994)] showed the rate to be two to three orders of magnitude higher. As a possible explanation of discrepancy, we consider the translational motion of the ends of the broken chains. Using a continuum approximation for the chain, we find that in the absence of friction, the rate of the process can be limited by the rate at which the two broken ends separate from one another and the lowering of the rate is at the most a factor of 2, for the parameters used in the simulation (for polyethylene). In the presence of friction, we find that the rate can be lowered by one to two orders of magnitude, making our results to be in reasonable agreement with the simulations.

Performance metrics in a hybrid MPI-OpenMP based molecular dynamics simulation with short-range interactions

We discuss the computational bottlenecks in molecular dynamics (MD) and describe the challenges in parallelizing the computation-intensive tasks. We present a hybrid algorithm using MPI (Message Passing Interface) with OpenMP threads for parallelizing a generalized MD computation scheme for systems with short range interatomic interactions. The algorithm is discussed in the context of nano-indentation of Chromium films with carbon indenters using the Embedded Atom Method potential for Cr-Cr interaction and the Morse potential for Cr-C interactions. We study the performance of our algorithm for a range of MPI-thread combinations and find the performance to depend strongly on the computational task and load sharing in the multi-core processor. The algorithm scaled poorly with MPI and our hybrid schemes were observed to outperform the pure message passing scheme, despite utilizing the same number of processors or cores in the cluster. Speed-up achieved by our algorithm compared favorably with that achieved by standard MD packages. (C) 2013 Elsevier Inc. All rights reserved.

Estimation of mechanical properties of single wall carbon nanotubes using molecular mechanics approach

Molecular mechanics based finite element analysis is adopted in the current work to evaluate the mechanical properties of Zigzag, Armchair and Chiral Single wall Carbon Nanotubes (SWCNT) of different diameters and chiralities. Three different types of atomic bonds, that is Carbon Carbon covalent bond and two types of Carbon Carbon van der Waals bonds are considered in the carbon nanotube system. The stiffness values of these bonds are calculated using the molecular potentials, namely Morse potential function and Lennard-Jones interaction potential function respectively and these stiffness's are assigned to spring elements in the finite element model of the CNT. The geometry of CNT is built using a macro that is developed for the finite element analysis software. The finite element model of the CNT is constructed, appropriate boundary conditions are applied and the behavior of mechanical properties of CNT is studied.

Modeling of Channel Potential and Subthreshold Slope of Symmetric Double-Gate Transistor

A new physically based classical continuous potential distribution model, particularly considering the channel center, is proposed for a short-channel undoped body symmetrical double-gate transistor. It involves a novel technique for solving the 2-D nonlinear Poisson's equation in a rectangular coordinate system, which makes the model valid from weak to strong inversion regimes and from the channel center to the surface. We demonstrated, using the proposed model, that the channel potential versus gate voltage characteristics for the devices having equal channel lengths but different thicknesses pass through a single common point (termed ``crossover point''). Based on the potential model, a new compact model for the subthreshold swing is formulated. It is shown that for the devices having very high short-channel effects (SCE), the effective subthreshold slope factor is mainly dictated by the potential close to the channel center rather than the surface. SCEs and drain-induced barrier lowering are also assessed using the proposed model and validated against a professional numerical device simulator.

Optimal barrier subdivision for Kramers' escape rate

We examine the effect of subdividing the potential barrier along the reaction coordinate on Kramers' escape rate for a model potential. Using the known supersymmetric potential approach, we show the existence of an optimal number of subdivisions that maximizes the rate.

Metallo crown porphyrins as ionophores-metal dependent uncoupling of mitochondrial energy potential

Porphyrins appended with crown ether moieties function as efficient uncouplesrs of oxidative phorphorylation in rat liver mitochondria. Permeation of these highly organized porphyrins decrease the respiratory coefficient index (RCI) values. Lowering of the RCI values parallels the number of K+ chelating crown ether groups attached to the porphyrins. The inhibitory effect upon the oxidative phorphorylation reaction depends on the nature of divalent metal ions, VO, Co, Cu and Zn in the porphyrin cavity and related to their relative tendency to complex intracellular K+ ions.

Metallo crown porphyrins as ionophores-metal dependent uncoupling of mitochondrial energy potential

Porphyrins appended with crown ether moieties function as efficient uncouplesrs of oxidative phorphorylation in rat liver mitochondria. Permeation of these highly organized porphyrins decrease the respiratory coefficient index (RCI) values. Lowering of the RCI values parallels the number of K+ chelating crown ether groups attached to the porphyrins. The inhibitory effect upon the oxidative phorphorylation reaction depends on the nature of divalent metal ions, VO, Co, Cu and Zn in the porphyrin cavity and related to their relative tendency to complex intracellular K+ ions.

Dynamics of Barrierless and Activated Chemical Reactions in a Dispersive Medium within the Fractional Diffusion Equation Approach

Barrierless chemical reactions have often been modeled as a Brownian motion on a one-dimensional harmonic potential energy surface with a position-dependent reaction sink or window located near the minimum of the surface. This simple (but highly successful) description leads to a nonexponential survival probability only at small to intermediate times but exponential decay in the long-time limit. However, in several reactive events involving proteins and glasses, the reactions are found to exhibit a strongly nonexponential (power law) decay kinetics even in the long time. In order to address such reactions, here, we introduce a model of barrierless chemical reaction where the motion along the reaction coordinate sustains dispersive diffusion. A complete analytical solution of the model can be obtained only in the frequency domain, but an asymptotic solution is obtained in the limit of long time. In this case, the asymptotic long-time decay of the survival probability is a power law of the Mittag−Leffler functional form. When the barrier height is increased, the decay of the survival probability still remains nonexponential, in contrast to the ordinary Brownian motion case where the rate is given by the Smoluchowski limit of the well-known Kramers' expression. Interestingly, the reaction under dispersive diffusion is shown to exhibit strong dependence on the initial state of the system, thus predicting a strong dependence on the excitation wavelength for photoisomerization reactions in a dispersive medium. The theory also predicts a fractional viscosity dependence of the rate, which is often observed in the reactions occurring in complex environments.

Polarographic and redox potential studies on copper(I) and copper(II) and their complexes. Part I. Copper(I and II)-ammonia and methylamine complexes

The equilibrium between cuprous ion, cupric ion and metallic copper has been studied using polarographic and redox potential measurements, by reducing cupric ion with copper gauze until equilibrium. Using the well-defined anodic diffusion current plateau, an amperometric method for estimating cuprous copper based on the titration of cuprous ion with dichromate or permanganate has been developed. The diffusion current constant and the disproportionation constant of cuprous ion and the standard potential for the reduction reaction of Cu2+ → Cu+ have been determined. Polarograms have been taken after reducing cupric complexes of ammonia and methylamine with copper until equilibrium. In the case of the copper-ammonia system, reduction to the cuprous state is practically complete while in the case of the cupric-methylamine system, the first cathodic wave occurs to some extent. A new method, called the polarographic-redox potential method, for determining the stability constants of cuprous and cupric complexes has been developed. The method depends upon the determination of the concentration of complexes by polarographic wave heights, and free cupric anc cuprous ions by redox potentials. The stability constants of the following complexes have been obtained: Cu(NH3)2+4, Cu(NH3)+2, Cu(CH3NH2)2(OH)2, Cu(CH3NH2)+2. The stability constants determined by the new method and the half-wave potential shift method agree and the value for the cupric-ammonia complex is in good agreement with Bjerrum method, indicating the reliability of this method.

Polarization Characteristics of Porous Electrode Systems with Adsorbed Intermediates Participating in the Electrode Reaction

Current-potential relationships are derived for porous electrode systems following a homogeneous model and whenadsorbed intermediates participate in the electrode reaction. Limiting Tafel slopes were deduced and compared with thecorresponding behavior on planar electrode systems. The theoretical results showed doubling of Tafel slopes when theslow-step is a charge-transfer reaction and a nonlogarithmic current-voltage behavior when the slow-step is a chemical reaction.Comparison of the experimental results with theory for the case of oxygen reduction on carbon surfaces in alkalinemedia indicates that a slow chemical reaction following the initial charge-transfer reaction to be the likely rate-controllingstep. Theoretical relationships are utilized to determine the exchange current density and the surface coverage by the adsorbedintermediates during the course of oxygen reduction from alkaline solutions on "carbon." Tafel slope measurementson planar and porous electrodes for the same reaction are suggested as one of the diagnostic criteria for elucidatingthe mechanistic pathways of electrochemical reactions.

Chronopotentiometry with power-law perturbation functions at an expanding plane electrode with and without a preceding blank period for systems with a coupled first-order homogeneous chemical reaction

The systems formalism is used to obtain the interfacial concentration transients for power-law current input at an expanding plane electrode. The explicit results for the concentration transients obtained here pertain to arbitrary homogeneous reaction schemes coupled to the oxidant and reductant of a single charge-transfer step and the power-law form without and with a preceding blank period (for two types of power-law current profile, say, (i) I(t) = I0(t−t0)q for t greater-or-equal, slanted t0, I(t) = 0 for t < t0; and (ii) I(t) = I0tq for t greater-or-equal, slanted t0, I(t) = 0 for t < t0). Finally the potential transients are obtained using Padé approximants. The results of Galvez et al. (for E, CE, EC, aC) (J. Electroanal. Chem., 132 (1982) 15; 146 (1983) 221, 233, 243), Molina et al. (for E) (J. Electroanal. Chem., 227 (1987) 1 and Kies (for E) (J. Electroanal. Chem., 45 (1973) 71) are obtained as special cases.

An assessment of the reduction potential of hydrogen plasma

Hydrogen plasma can be used for deoxidation of functional materials containing reactive metals in both bulk and thin film forms. Since the different species in the plasma are not in thermodynamic equilibrium, application of classical thermodynamics to the analysis of such a system is associated with some difficulties. While global equilibrium approaches have been tried, with and without additional approximations or constraints, there is some ambiguity in the results obtained. Presented in this article is the application of a local equilibrium concept to assess the thermodynamic limit of the reaction of each species present in the gas with oxides or oxygen dissolved in metals. Each reaction results in a different pal tial pressure of H2O. Because of the higher reactivity of the dissociated and ionized species and the larger thermodynamic driving force for reactions involving these species, they act as powerful reducing agents. It is necessary to remove the products of reaction from the plasma to prevent back reaction and gradual approach to global equilibrium. A quantitative description using the framework of the Ellingham-Richardson-Jeffes diagrams is presented.

Vibrational Spectra and Normal Coordinate Analysis of N-Methyl Thiourea

The infrared spectra of N-methylthiourea (NMTU) and its N-deuterated and S-methylated species were measured. Assignment of the infrared and Raman spectra of NMTU has been accomplished by correlation with thiourea and by use of infrared band shifts on N-deuteration as well as S-methylation. Normal coordinate analysis was performed for all the fundamentals of NMTU and NMTU-d3, the assignments obtained from the force field calculations being discussed in relation to those in other related thioureas and thioamides. The potential barriers to the internal rotations for the �NH2, �CH3, and �CN groups were estimated from the force constants.

Metabolome based reaction graphs of M.tuberculosis and M.leprae: A comparative network analysis

Background. Several types of networks, such as transcriptional, metabolic or protein-protein interaction networks of various organisms have been constructed, that have provided a variety of insights into metabolism and regulation. Here, we seek to exploit the reaction-based networks of three organisms for comparative genomics. We use concepts from spectral graph theory to systematically determine how differences in basic metabolism of organisms are reflected at the systems level and in the overall topological structures of their metabolic networks. Methodology/Principal Findings. Metabolome-based reaction networks of Mycobacterium tuberculosis, Mycobacterium leprae and Escherichia coli have been constructed based on the KEGG LIGAND database, followed by graph spectral analysis of the network to identify hubs as well as the sub-clustering of reactions. The shortest and alternate paths in the reaction networks have also been examined. Sub-cluster profiling demonstrates that reactions of the mycolic acid pathway in mycobacteria form a tightly connected sub-cluster. Identification of hubs reveals reactions involving glutamate to be central to mycobacterial metabolism, and pyruvate to be at the centre of the E. coli metabolome. The analysis of shortest paths between reactions has revealed several paths that are shorter than well established pathways. Conclusions. We conclude that severe downsizing of the leprae genome has not significantly altered the global structure of its reaction network but has reduced the total number of alternate paths between its reactions while keeping the shortest paths between them intact. The hubs in the mycobacterial networks that are absent in the human metabolome can be explored as potential drug targets. This work demonstrates the usefulness of constructing metabolome based networks of organisms and the feasibility of their analyses through graph spectral methods. The insights obtained from such studies provide a broad overview of the similarities and differences between organisms, taking comparative genomics studies to a higher dimension.

Dynamics of activationless reactions in solution

Recent picosecond and subpicosecond laser spectroscopy experiments have revealed several chemically and biologically important reactions in solution in which the reaction potential surface does not present a barrier to the motion along the reaction coordinate.The dynamics of these reactions display diverse and interesting behavior. They include the dependence of relaxation rate on the solvent viscosity, the solvent polarity, the temperature, and the wavelength of the exciting light. In this article we review the recent developments in the theoretical description of activationless processes in solution and compare them with the available experimental results