Dependence of folding rates on protein length

Using three-dimensional Go lattice models with side chains for proteins, we investigate the dependence of folding times on protein length. In agreement with previous theoretical predictions, we find that the folding time grows as a power law with the chain length N with exponent $\lambda \approx 3.6$ for the Go model, in which all native interactions (i.e., between all side chains and backbone atoms) are uniform. If the interactions between side chains are given by pairwise statistical potentials, which introduce heterogeneity in the contact energies, then the power law fits yield large $\lambda$ values that typically signifies a crossover to an underlying activated process. Accordingly, the dependence of folding time is best described by the stretched exponential \exp(\sqrt{N}). The study also shows that the incorporation of side chains considerably slows down folding by introducing energetic and topological frustration.Comment: 6 pages, 5 eps figure

Probing the Mechanisms of Fibril Formation Using Lattice Models

Using exhaustive Monte Carlo simulations we study the kinetics and mechanism of fibril formation using lattice models as a function of temperature and the number of chains. While these models are, at best, caricatures of peptides, we show that a number of generic features thought to govern fibril assembly are present in the toy model. The monomer, which contains eight beads made from three letters (hydrophobic, polar, and charged), adopts a compact conformation in the native state. The kinetics of fibril assembly occurs in three distinct stages. In each stage there is a cascade of events that transforms the monomers and oligomers to ordered structures. In the first "burst" stage highly mobile oligomers of varying sizes form. The conversion to the aggregation-prone conformation occurs within the oligomers during the second stage. As time progresses, a dominant cluster emerges that contains a majority of the chains. In the final stage, the aggregation-prone conformation particles serve as a template onto which smaller oligomers or monomers can dock and undergo conversion to fibril structures. The overall time for growth in the latter stages is well described by the Lifshitz-Slyazov growth kinetics for crystallization from super-saturated solutions.Comment: 27 pages, 6 figure

Periodic force induced stabilization or destabilization of the denatured state of a protein

We have studied the effects of an external sinusoidal force in protein folding kinetics. The externally applied force field acts on the each amino acid residues of polypeptide chains. Our simulation results show that mean protein folding time first increases with driving frequency and then decreases passing through a maximum. With further increase of the driving frequency the mean folding time starts increasing as the noise-induced hoping event (from the denatured state to the native state) begins to experience many oscillations over the mean barrier crossing time period. Thus unlike one-dimensional barrier crossing problems, the external oscillating force field induces both \emph{stabilization or destabilization of the denatured state} of a protein. We have also studied the parametric dependence of the folding dynamics on temperature, viscosity, non-Markovian character of bath in presence of the external field

An improved system to measure leaf gas exchange on adaxial and abaxial surfaces

Measurement of leaf carbon gain and water loss (gas exchange) in planta is a standard procedure in plant science research for attempting to understand physiological traits related to water use and photosynthesis. Leaves carry out gas exchange through the upper (adaxial) and lower (abaxial) surfaces at different magnitudes, depending on the stomatal density, stomatal aperture, cuticular permeability, etc., of each surface, which we account for in gas exchange parameters such as stomatal conductance. Most commercial devices measure leaf gas exchange by combining the adaxial and abaxial fluxes and calculating bulk gas exchange parameters, missing details of the plant's physiological response on each side. Additionally, the widely used equations to estimate gas exchange parameters neglect the contribution of small fluxes such as cuticular conductance, adding extra uncertainties to measurements performed in water-stress or low-light conditions. Accounting for the gas exchange fluxes from each side of the leaf allows us to better describe plants' physiological traits under different environmental conditions and account for genetic variability. Here, apparatus and materials are presented for adapting two LI-6800 Portable Photosynthesis Systems to work as one gas exchange system to measure adaxial and abaxial gas exchange simultaneously. The modification includes a template script with the equations to account for small fluxes. Instructions are provided for incorporating the add-on script into the device's computational sequence, display, variables, and spreadsheet results. We explain the method to obtain an equation to estimate boundary layer conductance to water for the new setup and how to embed this equation in the devices' calculations using the provided add-on script. The apparatus, methods, and protocols presented here provide a simple adaptation combining two LI-6800s to obtain an improved system to measure leaf gas exchange on adaxial and abaxial surfaces

A guide to chemokines and their receptors

The chemokines (or chemotactic cytokines) are a large family of small, secreted proteins that signal through cell surface G‐protein coupled heptahelical chemokine receptors. They are best known for their ability to stimulate the migration of cells, most notably white blood cells (leukocytes). Consequently, chemokines play a central role in the development and homeostasis of the immune system, and are involved in all protective or destructive immune and inflammatory responses. Classically viewed as inducers of directed chemotactic migration, it is now clear that chemokines can stimulate a variety of other types of directed and undirected migratory behaviour, such as haptotaxis, chemokinesis, and haptokinesis, in addition to inducing cell arrest or adhesion. However, chemokine receptors on leukocytes can do more than just direct migration, and these molecules can also be expressed on, and regulate the biology of, many non‐leukocytic cell types. Chemokines are profoundly affected by post‐translational modification, by interaction with the extracellular matrix (ECM), and by binding to heptahelical ‘atypical’ chemokine receptors that regulate chemokine localisation and abundance. This guide gives a broad overview of the chemokine and chemokine receptor families; summarises the complex physical interactions that occur in the chemokine network; and, using specific examples, discusses general principles of chemokine function, focussing particularly on their ability to direct leukocyte migration

Scoping study on natural resources and climate change in Southeast Asia with a focus on agriculture. Final report

Climate change / Natural resources / Environmental effects / Agroecology / Agricultural production / Crops / Cropping systems / Farming systems / Livestock / Fisheries / Food security / Water management / Economic aspects / Rural poverty / Policy / Nutrient management / South East Asia / Cambodia / Laos / Thailand / Vietnam / Myanmar / China / Greater Mekong Subregion / Tonle Sap / Yunnan

Von Neumann's Quantization of General Relativity

Von Neumann's procedure is applied for quantization of General Relativity. We quantize the initial data of dynamical variables at the Planck epoch, where the Hubble parameter coincides with the Planck mass. These initial data are defined via the Fock simplex in the tangent Minkowskian space-time and the Dirac conformal interval. The Einstein cosmological principle is applied for the average of the spatial metric determinant logarithm over the spatial volume of the visible Universe. We derive the splitting of the general coordinate transformations into the diffeomorphisms (as the object of the second N\"other theorem) and the initial data transformations (as objects of the first N\"other theorem). Following von Neumann, we suppose that the vacuum state is a quantum ensemble. The vacuum state is degenerated with respect to quantum numbers of non-vacuum states with the distribution function that yields the Casimir effect in gravidynamics in analogy to the one in electrodynamics. The generation functional of the perturbation theory in gravidynamics is given as a solution of the quantum energy constraint. We discuss the region of applicability of gravidynamics and its possible predictions for explanation of the modern observational and experimental data.Comment: 14 pages, updated version with extended discussio