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

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

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

Nonlinear interaction between electromagnetic fields at high temperature

The electron-positron `box' diagram produces an effective action which is fourth order in the electromagnetic field. We examine the behaviour of this effective action at high-temperature (in analytically continued imaginary-time thermal perturbation theory). We argue that there is a finite, nonzero limit as $T\rightarrow \infty$ (where $T$ is the temperature). We calculate this limit in the nonrelativistic static case, and in the long-wavelength limit. We also briefly discuss the self-energy in 2-dimensional QED, which is similar in some respects.Comment: 13 pages, DAMTP 94/3

Sequencing of folding events in Go-like proteins

We have studied folding mechanisms of three small globular proteins: crambin (CRN), chymotrypsin inhibitor 2 (CI2) and the fyn Src Homology 3 domain (SH3) which are modelled by a Go-like Hamiltonian with the Lennard-Jones interactions. It is shown that folding is dominated by a well-defined sequencing of events as determined by establishment of particular contacts. The order of events depends primarily on the geometry of the native state. Variations in temperature, coupling strengths and viscosity affect the sequencing scenarios to a rather small extent. The sequencing is strongly correlated with the distance of the contacting aminoacids along the sequence. Thus $\alpha$-helices get established first. Crambin is found to behave like a single-route folder, whereas in CI2 and SH3 the folding trajectories are more diversified. The folding scenarios for CI2 and SH3 are consistent with experimental studies of their transition states.Comment: REVTeX, 12 pages, 11 EPS figures, J. Chem. Phys (in press

QED Corrections to Planck's Radiation Law and Photon Thermodynamics

Leading corrections to Planck's formula and photon thermodynamics arising from the pair-mediated photon-photon interaction are calculated. This interaction is attractive and causes an increase in occupation number for all modes. Possible consequences, including the role of the cosmic photon gas in structure formation, are considered.Comment: 15 pages, Revtex 3.

Collapse of Randomly Self-Interacting Polymers

We use complete enumeration and Monte Carlo techniques to study self--avoiding walks with random nearest--neighbor interactions described by $v_0q_iq_j$, where $q_i=\pm1$ is a quenched sequence of ``charges'' on the chain. For equal numbers of positive and negative charges ($N_+=N_-$), the polymer with $v_0>0$ undergoes a transition from self--avoiding behavior to a compact state at a temperature $\theta\approx1.2v_0$. The collapse temperature $\theta(x)$ decreases with the asymmetry $x=|N_+-N_-|/(N_++N_-)$Comment: 8 pages, TeX, 4 uuencoded postscript figures, MIT-CMT-

One-loop self-energy correction to the 1s and 2s hyperfine splitting in H-like systems

The one-loop self-energy correction to the hyperfine splitting of the 1s and 2s levels in H-like low-Z atoms is evaluated to all orders in Z\alpha. The results are compared to perturbative calculations. The residual higher-order contribution is evaluated. Implications to the specific difference of the hyperfine structure intervals 8\Delta \nu_2 - \Delta \nu_1 in He^+ are investigated.Comment: 17 pages, RevTeX, 3 figure

Conformations of Proteins in Equilibrium

We introduce a simple theoretical approach for an equilibrium study of proteins with known native state structures. We test our approach with results on well-studied globular proteins, Chymotrypsin Inhibitor (2ci2), Barnase and the alpha spectrin SH3 domain and present evidence for a hierarchical onset of order on lowering the temperature with significant organization at the local level even at high temperatures. A further application to the folding process of HIV-1 protease shows that the model can be reliably used to identify key folding sites that are responsible for the development of drug resistance .Comment: 6 pages, 3 eps figure