Four-states phase diagram of proteins

A four states phase diagram for protein folding as a function of temperature and solvent quality is derived from an improved 2-d lattice model taking into account the temperature dependence of the hydrophobic effect. The phase diagram exhibits native, globule and two coil-type regions. In agreement with experiment, the model reproduces the phase transitions indicative of both warm and cold denaturations. Finally, it predicts transitions between the two coil states and a critical point.Comment: 7 pages, 5 figures. Accepted for publication in Europhysics Letter

Prospects for Plug-in Hybrid Electric Vehicles in the United States and Japan: A General Equilibrium Analysis

Abstract and PDF report are also available on the MIT Joint Program on the Science and Policy of Global Change website (http://globalchange.mit.edu/)The plug-in hybrid electric vehicle (PHEV) may offer a potential near term, low carbon alternative to today's gasoline- and diesel-powered vehicles. A representative vehicle technology that runs on electricity in addition to conventional fuels was introduced into the MIT Emissions Prediction and Policy Analysis (EPPA) model as a perfect substitute for internal combustion engine (ICE-only) vehicles in two likely early-adopting markets, the United States and Japan. We investigate the effect of relative vehicle cost and all-electric range on the timing of PHEV market entry in the presence and absence of an advanced cellulosic biofuels technology and a strong (450ppm) economy-wide carbon constraint. Vehicle cost could be a significant barrier to PHEV entry unless fairly aggressive goals for reducing battery costs are met. If a low cost vehicle is available we find that the PHEV has the potential to reduce CO2 emissions, refined oil demand, and under a carbon policy the required CO2 price in both the United States and Japan. The emissions reduction potential of PHEV adoption depends on the carbon intensity of electric power generation and the size of the vehicle fleet. Thus, the technology is much more effective in reducing CO2 emissions if adoption occurs under an economy-wide cap and trade system that also encourages low-carbon electricity generation.BP Conversion Research Project and the MIT Joint Program on the Science and Policy of Global Change through a consortium of industrial sponsors and Federal grants

Molecular dynamics of folding of secondary structures in Go-type models of proteins

We consider six different secondary structures of proteins and construct two types of Go-type off-lattice models: with the steric constraints and without. The basic aminoacid-aminoacid potential is Lennard Jones for the native contacts and a soft repulsion for the non-native contacts. The interactions are chosen to make the target secondary structure be the native state of the system. We provide a thorough equilibrium and kinetic characterization of the sequences through the molecular dynamics simulations with the Langevin noise. Models with the steric constraints are found to be better folders and to be more stable, especially in the case of the $\beta$-structures. Phononic spectra for vibrations around the native states have low frequency gaps that correlate with the thermodynamic stability. Folding of the secondary structures proceeds through a well defined sequence of events. For instance, $\alpha$-helices fold from the ends first. The closer to the native state, the faster establishment of the contacts. Increasing the system size deteriorates the folding characteristics. We study the folding times as a function of viscous friction and find a regime of moderate friction with the linear dependence. We also consider folding when one end of a structure is pinned which imitates instantaneous conditions when a protein is being synthesized. We find that, under such circumstances, folding of helices is faster and of the $\beta$-sequences slower.Comment: REVTeX, 14 pages, EPS figures included, JCP in pres

Cherenkov radiation by particles traversing the background radiatio n

High energy particles traversing the Universe through the cosmic microwave backgroung radiation can, in principle, emit Cherenkov radiation. It is shown that the energy threshold for this radiation is extremely high and its intensity would be too low due to the low density of the "relic photons gas" and very weak interaction of two photons.Comment: 6 pages, LATEX, no Figs.; to be published in JETP Lett. 75 (N4) (2002

Combining a New Vehicle Fuel Economy Standard with a Cap-and-Trade Policy: Energy and Economic Impact in the United States

http://globalchange.mit.edu/research/publications/2271The United States has adopted fuel economy standards that require increases in the on-road efficiency of new passenger vehicles, with the goal of reducing petroleum use, as well as (more recently) greenhouse gas (GHG) emissions. Understanding the cost and effectiveness of this policy, alone and in combination with economy-wide policies that constrain GHG emissions, is essential to inform coordinated design of future climate and energy policy. In this work we use a computable general equilibrium model, the MIT Emissions Prediction and Policy Analysis (EPPA) model, to investigate the effect of combining a fuel economy standard with an economy-wide GHG emissions constraint in the United States. First, a fuel economy standard is shown to be at least five to fourteen times less cost effective than a price instrument (fuel tax) when targeting an identical reduction in cumulative gasoline use. Second, when combined with a cap-and-trade (CAT) policy, the fuel economy standard increases the cost of meeting the GHG emissions constraint by forcing expensive reductions in passenger vehicle gasoline use, displacing more cost-effective abatement opportunities. Third, the impact of adding a fuel economy standard to the CAT policy depends on the availability and cost of abatement opportunities in transport—if advanced biofuels provide a cost-competitive, low carbon alternative to gasoline, the fuel economy standard does not bind and the use of low carbon fuels in passenger vehicles makes a significantly larger contribution to GHG emissions abatement relative to the case when biofuels are not available. This analysis underscores the potentially large costs of a fuel economy standard relative to alternative policies aimed at reducing petroleum use and GHG emissions. It also demonstrates the importance of jointly considering the effects of multiple policies aimed at reducing petroleum use and GHG emissions, and the associated economic costs

Unfolding Rates for the Diffusion-Collision Model

In the diffusion-collision model, the unfolding rates are given by the likelihood of secondary structural cluster dissociation. In this work, we introduce an unfolding rate calculation for proteins whose secondary structural elements are $\alpha$-helices, modeled from thermal escape over a barrier which arises from the free energy in buried hydrophobic residues. Our results are in good agreement with currently accepted values for the attempt rate.Comment: Shorter version of cond-mat/0011024 accepted for publication in PR

Equity and Emissions Trading in China

China has embarked on an ambitious pathway for establishing a national carbon market in the next five to ten years. In this study, we analyze the distributional aspects of a Chinese emissions-trading scheme from ethical, economic, and stated-preference perspectives. We focus on the role of emissions permit allocation and first show how specific equity principles can be incorporated into the design of potential allocation schemes. We then assess the economic and distributional impacts of those allocation schemes using a computable general equilibrium model with regional detail for the Chinese economy. Finally, we conduct a survey among Chinese climate-policy experts on the basis of the simulated model impacts. The survey participants indicate a relative preference for allocation schemes that put less emissions-reduction burden on the western provinces, a medium burden on the central provinces, and a high burden on the eastern provinces. Most participants show strong support for allocating emissions permits based on consumption-based emissions responsibilities

Applying Engineering and Fleet Detail to Represent Passenger Vehicle Transport in a Computable General Equilibrium Model

http://globalchange.mit.edu/research/publications/2270A well-known challenge in computable general equilibrium (CGE) models is to maintain correspondence between the forecasted economic and physical quantities over time. Maintaining such a correspondence is necessary to understand how economic forecasts reflect, and are constrained by, relationships within the underlying physical system. This work develops a method for projecting global demand for passenger vehicle transport, retaining supplemental physical accounting for vehicle stock, fuel use, and greenhouse gas (GHG) emissions. This method is implemented in the MIT Emissions Prediction and Policy Analysis Version 5 (EPPA5) model and includes several advances over previous approaches. First, the relationship between per-capita income and demand for passenger vehicle transport services (in vehicle-miles traveled, or VMT) is based on econometric data and modeled using quasi-homothetic preferences. Second, the passenger vehicle transport sector is structured to capture opportunities to reduce fleet-level gasoline use through the application of vehicle efficiency or alternative fuel vehicle technologies, introduction of alternative fuels, or reduction in demand for VMT. Third, alternative fuel vehicles (AFVs) are introduced into the EPPA model. Fixed costs as well as learning effects that could affect the rate of AFV introduction are captured explicitly. This model development lays the foundation for assessing policies that differentiate based on vehicle age and efficiency, alter the relative prices of fuels, or focus on promoting specific advanced vehicle or fuel technologies

Consumption-Based Adjustment of China's Emissions-Intensity Targets: An Analysis of its Potential Economic Effects

China’s Twelfth Five-Year Plan (2011–2015) aims to achieve a national carbon intensity reduction of 17% through differentiated targets at the provincial level. Allocating the national target among China’s provinces is complicated by the fact that more than half of China’s national carbon emissions are embodied in interprovincial trade, with the relatively developed eastern provinces relying on the central and western provinces for energy-intensive imports. This study develops a consistent methodology to adjust regional emissions-intensity targets for trade-related emissions transfers and assesses its economic effects on China's provinces using a regional computable general equilibrium model of the Chinese economy. This study finds that in 2007 China's eastern provinces outsource 14% of their territorial emissions to the central and western provinces. Adjusting the provincial targets for those emissions transfers increases the reduction burden for the eastern provinces by 60%, while alleviating the burden for the central and western provinces by 50% each. The CGE analysis indicates that this adjustment could double China's national welfare loss compared to the homogenous and politics-based distribution of reduction targets. A shared-responsibility approach that balances production-based and consumption-based emissions responsibilities is found to alleviate those unbalancing effects and lead to a more equal distribution of economic burden among China's provinces.The authors gratefully acknowledge the financial support for this work provided by the MIT Joint Program on the Science and Policy of Global Change through a consortium of industrial sponsors and Federal grants, and by the AXA Research Fund which is supporting Marco Springmann's doctoral research. We further thank Eni S.p.A., ICF International, Shell International Limited, and the French Development Agency (AFD), founding sponsors of the China Energy and Climate Project. We also grateful for support provided by the Social Science Key Research Program from National Social Science Foundation, China of Grant No. 09&ZD029 and by Rio Tinto China. We would further like to thank John Reilly, Sergey Paltsev, Henry Jacoby and Audrey Resutek for helpful comments, discussion and edits