Stochastic kinetics of a single headed motor protein: dwell time distribution of KIF1A

KIF1A, a processive single headed kinesin superfamily motor, hydrolyzes Adenosine triphosphate (ATP) to move along a filamentous track called microtubule. The stochastic movement of KIF1A on the track is characterized by an alternating sequence of pause and translocation. The sum of the durations of pause and the following translocation defines the dwell time. Using the NOSC model (Nishinari et. al. PRL, {\bf 95}, 118101 (2005)) of individual KIF1A, we systematically derive an analytical expression for the dwell time distribution. More detailed information is contained in the probability densities of the "conditional dwell times" $\tau_{\pm\pm}$ in between two consecutive steps each of which could be forward (+) or backward (-). We calculate the probability densities $\Xi_{\pm\pm}$ of these four conditional dwell times. However, for the convenience of comparison with experimental data, we also present the two distributions $\Xi_{\pm}^{*}$ of the times of dwell before a forward (+) and a backward (-) step. In principle, our theoretical prediction can be tested by carrying out single-molecule experiments with adequate spatio-temporal resolution.Comment: Author-edited final version published in EP

High value products, supermarkets and vertical arrangements in Indonesia

" Indonesian economy has experienced some major changes during the last three decades and transformed from a predominantly agricultural economy to one that relies more heavily on its non-agricultural sector. Within agriculture, there has also been a change in the contribution of different sub sectors and high value products have grown relatively rapidly making agriculture more diversified. Similar to the changes in agricultural production, food consumption in Indonesia has shown a pattern of change over the past three decades, from a diet characterized primarily by the staple foods of cereals and cassava, to one that includes a larger share of fruits, fish, meats, dairy products and processed foods. Alongside the change in composition of food demand, newer forms of retail have also come up commonly known as supermarkets. However, the emergence of modern retailing has other consequences that go beyond consumers. It requires deep integration with farmers and can influence the production and transaction costs at farm level. It can also influence the distribution of value among different agents involved in production, intermediation, and retailing. In this paper we pursue three interrelated objectives. First, we review the structural changes that have taken place in Indonesian agriculture for the last three decades and the state of high value products. Second, we examine the driving forces behind the production of high value products and the constraints that limit their production. Third, we review the emergence of supermarkets and the vertical arrangements among farmers, traders/distributors, and supermarkets. We have relied both on primary and secondary data sources. Most of the secondary data has come from government directorates, different ministries and the central bureau of statistics (CBS) of the Government of Indonesia. In cases where secondary information was not readily available, we have also collected primary data. Our findings suggest that during the last three decades, there has been a significant structural change in Indonesian agriculture and the production of high value commodities and products –estate crops, livestock, fisheries, fruits and vegetables, and floriculture – has grown faster than the cereals. However, the extent of diversification towards high value products has remained limited to few regions and to few products within each sub sector. Factors that have contributed most in diversification are the rapid growth in income and accompanied changes in urban consumption in favor of high value products and agricultural mechanization. The economic crisis that was triggered by the currency crisis has had a long negative impact on agriculture sector. Structural changes in Indonesian agriculture have been accompanied by changes in consumption pattern in urban areas in favor of high value products and by a major change in retailing in the form of growth of modern supermarkets. To cater to the demand of changed urban consumption needs, supermarkets have been integrating with farmers through formal and informal contracts. This vertical relationship between farms and supermarkets that has been emerging in Indonesia has been helpful to follow grades and standards, to improve quality, and to reduce transaction costs and information asymmetries. It has also been helpful to reduce price and production risks at farm level and to ensure a higher price for farmers compared to traditional value chain. However, it seems that the participation of small holders in the vertical relationship depends largely on vendors. Within the vertical chain, supermarkets appropriate a monopsony rent. Important policies that can be drawn from this study are the greater emphasize on rural infrastructure, user right of state-owned estate to smallholders, promotion of public-private partnerships, encouragements of vertical arrangements, grades and standards, and bringing up the modern retailing sector under the purview of regulatory oversights." Authors' AbstractDiet ,High value agricultural products ,Supermarkets ,

Competitive partial equilibrium analysis of U.S. agriculture under alternative energy and export situations - application of separable and chance constrained programming

As an energy source for machinery operations, irrigation, crop drying and manufacture of fertilizer and agricultural chemicals, fossil fuels form a critical group of inputs in crop production. In the United States, agricultural exports are becoming increasingly important in balancing trade deficits caused by imported energy. A national quadratic programming model is used in this study to analyze the impact of alternative energy price and agricultural export situations on U.S. agriculture in the year 1985. The model is solved by using separable programming. Uncertainty incorporated in export, the model also is solved under a chance constrained programming framework. The model simulates a pure competition situation in agriculture. Mainland U.S. is divided into 105 agriculturally homogeneous producing areas, which are aggregated into nine market regions. Linear demand functions for barley, corn, oats, wheat, and soybean and cottonseed oil are incorporated in the model. The production submodel represents production of food and feed grains, oil and fiber crops, hay and silage, and oil meal in a linear programming framework. The livestock sector is handled exogenously. Transportation is defined for food and feed grains, oil, and oil meal among the nine market regions. Land, water, nitrogen, and energy are the inputs explicitly considered in the model. Diesel fuel, gasoline, natural gas, electricity, and liquid petroleum gas are the energy sources considered. When solved, the model estimated the impacts of alternative energy and export situations on interregional distribution of crop production, allocation of various inputs, prices of agricultural commodities and farm incomes. The impacts are measured at national and regional levels;The model results indicate that as the export levels increase, more pressure is developed on the resources like land and water which are fixed in supply. Consequently, rental prices of these resources increase. Also, the prices of crop commodities increase causing a higher food cost for the consumers. Farm sector, however, realizes a higher net income because of the increased export levels;With the increase in energy prices, use of energy intensive inputs are substituted by nonintensive energy inputs. Thus, whereas more dry cropland is estimated to be used under increased energy prices, the use of irrigated cropland, nitrogen, and water for irrigation reduces. Rental prices for land and water increase with the increase in energy prices. Crop commodity supply, however, decreases and as a consequence higher prices for the crop commodities result. Because of the price inelastic demand structure of the crop commodities, consumer food costs increase by a considerable amount. Also, it is estimated that farm sector not only covers the increased costs of production due to higher energy prices, but because of the very inelastic demand for the crop commodities it actually gains in its income from an increase in the energy prices. The gain is, however, not distributed in the same proportion among all the farm regions. The position of a particular region in the distribution depends on its efficiency in energy input use and the type of crop it is growing

The Rise of Supermarkets and Vertical Relationships in the Indonesian Food Value Chain: Causes and Consequences

This paper reviews the causes of the emergence of modern retailing and the vertical relationships in the Indonesian food value chain, and the consequences of these changes on market organization and value distribution. The findings of this paper suggest that there are both demand- and supply-side factors that contribute to the emergence of modern retailing. The evolution of vertical relationships between farmers and modern retailers observed in Indonesia is a direct response to risks and quality uncertainty. In the vertical relation, large-scale retailers may earn a monopsonistic rent, and there are risks of exclusion of small-scale farmers from the emerging food value chain. However, there are alternative channels through which farmers may sell their products, albeit at a lower price compared to the modern channels, and measures can be instituted to protect them against monopsonistic rents. The findings have important policy implications for developing countries.supermarkets, retailing, Indonesia, food value chain

Intra-cellular transport by single-headed kinesin KIF1A: effects of single-motor mechano-chemistry and steric interactions

In eukaryotic cells, many motor proteins can move simultaneously on a single microtubule track. This leads to interesting collective phenomena like jamming. Recently we reported ({\it Phys. Rev. Lett. {\bf 95}, 118101 (2005)}) a lattice-gas model which describes traffic of unconventional (single-headed) kinesins KIF1A. Here we generalize this model, introducing a novel interaction parameter $c$, to account for an interesting mechano-chemical process which has not been considered in any earlier model. We have been able to extract all the parameters of the model, except $c$, from experimentally measured quantities. In contrast to earlier models of intra-cellular molecular motor traffic, our model assigns distinct ``chemical'' (or, conformational) states to each kinesin to account for the hydrolysis of ATP, the chemical fuel of the motor. Our model makes experimentally testable theoretical predictions. We determine the phase diagram of the model in planes spanned by experimentally controllable parameters, namely, the concentrations of kinesins and ATP. Furthermore, the phase-separated regime is studied in some detail using analytical methods and simulations to determine e.g. the position of shocks. Comparison of our theoretical predictions with experimental results is expected to elucidate the nature of the mechano-chemical process captured by the parameter $c$.Comment: 17 pages including 14 embedded EPS figures; accepted for publication in Physical Review

Traffic of single-headed motor proteins KIF1A: effects of lane changing

KIF1A kinesins are single-headed motor proteins which move on cylindrical nano-tubes called microtubules (MT). A normal MT consists of 13 protofilaments on which the equispaced motor binding sites form a periodic array. The collective movement of the kinesins on a MT is, therefore, analogous to vehicular traffic on multi-lane highways where each protofilament is the analogue of a single lane. Does lane-changing increase or decrease the motor flux per lane? We address this fundamental question here by appropriately extending a recent model [{\it Phys. Rev. E {\bf 75}, 041905 (2007)}]. By carrying out analytical calculations and computer simulations of this extended model, we predict that the flux per lane can increase or decrease with the increasing rate of lane changing, depending on the concentrations of motors and the rate of hydrolysis of ATP, the ``fuel'' molecules. Our predictions can be tested, in principle, by carrying out {\it in-vitro} experiments with fluorescently labelled KIF1A molecules.Comment: 4 pages REVTEX with 4 EPS figures; new schematic figure of the mode

Finite Element Simulation ForThermal Analysis In Laser Forming Of D36 Ship Building Steel

The laser bending process is one of the advanced bending processes which can be achieved by elasto-plastic deformation through the local introduction of thermal stresses. It is a thermo-mechanical process in which a laser heat source of suitable power is used for bending the material rather than any external force. In this work, sequential thermal analysis is carried out for SOLID70 element by using ANSYS. The deformation of a sheet, subjected to an irradiation, has been studied through a sequentially coupled thermo-mechanical elasto-plastic simulation by using the finite element model (FEM). D36 shipbuilding steel sheet has been taken as the work-piece material for the analysis. The thermal effects due to heat input into the work piece are analyzed which includes temperature distribution, thermal flux distribution, thermal gradient distribution and variation of thermal properties with time.Keywords: Laser beam forming, Gaussian distribution, FEM

Stochastic kinetics of ribosomes: single motor properties and collective behavior

Synthesis of protein molecules in a cell are carried out by ribosomes. A ribosome can be regarded as a molecular motor which utilizes the input chemical energy to move on a messenger RNA (mRNA) track that also serves as a template for the polymerization of the corresponding protein. The forward movement, however, is characterized by an alternating sequence of translocation and pause. Using a quantitative model, which captures the mechanochemical cycle of an individual ribosome, we derive an {\it exact} analytical expression for the distribution of its dwell times at the successive positions on the mRNA track. Inverse of the average dwell time satisfies a ``Michaelis-Menten-like'' equation and is consistent with the general formula for the average velocity of a molecular motor with an unbranched mechano-chemical cycle. Extending this formula appropriately, we also derive the exact force-velocity relation for a ribosome. Often many ribosomes simultaneously move on the same mRNA track, while each synthesizes a copy of the same protein. We extend the model of a single ribosome by incorporating steric exclusion of different individuals on the same track. We draw the phase diagram of this model of ribosome traffic in 3-dimensional spaces spanned by experimentally controllable parameters. We suggest new experimental tests of our theoretical predictions.Comment: Final published versio