A coarse-grained protein model in a water-like solvent

Simulations employing an explicit atom description of proteins in solvent can be computationally expensive. On the other hand, coarse-grained protein models in implicit solvent miss essential features of the hydrophobic effect, especially its temperature dependence and have limited ability to capture the kinetics of protein folding. We propose a free space two-letter protein (“H-P”) model in a simple, but qualitatively accurate description for water, the Jagla model, which coarse-grains water into an isotropically interacting sphere. Using Monte Carlo simulations, we design protein-like sequences that can undergo a collapse, exposing the “Jagla-philic” monomers to the solvent, while maintaining a “hydrophobic” core. This protein-like model manifests heat and cold denaturation in a manner that is reminiscent of proteins. While this protein-like model lacks the details that would introduce secondary structure formation, we believe that these ideas represent a first step in developing a useful, but computationally expedient, means of modeling proteins.We thank C. A. Angell, M. Marques, S. Sastry, and Z. Yan for helpful discussions. S. S. and S. K. K. acknowledge the DOE - Basic Engineering Sciences for funding this research. P. G. D. gratefully acknowledges the support of the National Science Foundation (Grant CHE-1213343). P.J.R. gratefully acknowledges the support of the National Science Foundation (Collaborative Research Grants CHE-0908265 and CHE-0910615). Additional support from the R.A. Welch Foundation (F-0019) to P.J.R. is also gratefully acknowledged. HES thanks the NSF Chemistry Division for support through grants CHE 0911389, CHE 0908218 and CHE-1213217. S. V. B. acknowledges the partial support of this research through the Dr Bernard W. Gamson Computational Science Center at Yeshiva College. (DOE - Basic Engineering Sciences; CHE-1213343 - National Science Foundation; CHE-0908265 - National Science Foundation; CHE-0910615 - National Science Foundation; F-0019 - R.A. Welch Foundation; CHE 0911389 - NSF Chemistry Division; CHE 0908218 - NSF Chemistry Division; CHE-1213217 - NSF Chemistry Division; Dr Bernard W. Gamson Computational Science Center at Yeshiva College)Published versio

Analog Computer Simulation of the Runoff Characteristics of an Urban Watershed

In the syntheses of hydrograph characteristics of small urban watersheds, the distribution of water among the various phases of the runoff process is attempted by the concept of equivalent rural watershed. The urban parameters considered in the study are percentage impervious cover and characteristic impervious length factor. A mathematical model is developed for the equivalent rural watershed with precipitation as input. The hydrograph of outflow is obtained by chronologically deducting the losses due to interception, infiltration, and depression storages from precipitation and then routing through the watershed storage. This mathematical procedure is programmed on an analog computer and is tested with data from the Waller Creek watershed, at Austin, Texas. In the verification process, watershed coefficients representing interception, infiltration, and depression storage are established by trial and error such that the simulated and observed hydrographs are nearly identical with a high statistical correlation. Sensitivity studies indicate the relative influence of the watershed coefficients on the runoff process. The watershed coefficients determined by model verification for each year of study are related to corresponding urban parameters

K -\u3epi pi electroweak penguins in the chiral limit

We report on dispersive and finite energy sum rule analyses of the electroweak penguin matrix elements left angle bracket(ππ)2|Q7,8|K0right-pointing angle bracket in the chiral limit. We accomplish the correct perturbative matching (scale and scheme dependence) at NLO in αs, and we describe two different strategies for numerical evaluation

Equivariant differential characters and symplectic reduction

We describe equivariant differential characters (classifying equivariant circle bundles with connections), their prequantization, and reduction

Relating B_s Mixing and B_s -> mu+mu- with New Physics

We perform a study of the Standard Model (SM) fit to the mixing quantities $\Delta M_{B_s}$, and $\Delta \Gamma_{B_s}/\Delta M_{B_s}$ in order to bound contributions of New Physics to $B_s$ mixing. We then use this to explore the branching fraction of $B_{s} \to \mu^+\mu^-$ in certain models of New Physics (NP). In most cases, this constrains NP amplitudes for $B_{s} \to \mu^+\mu^-$ to lie below the SM component.Comment: 27 pages, 5 figures; corrected misprints, updated numerical inputs and new reference

Natural Salinity Removal Processes in Reservoirs

A small but significant amount of salinity removal has been reported by various authors to occur in mainstem Colorado River reservoirs. Recalculation of some of these salinity budgets, together with a review of the data bases used, usggests taht removal has not often been conclusively demonstrated. Laboratory microcosm experiments and field data indicate that calcium carbonate precipitation, perhaps with some coprecipitation of magnesium carbonate, is the mechanism responsible for most of the salinity removal in Oneida Reservoir, Idaho. Coprecipitation processes (including ion exchange), coagulation, and bioassimilation do not appear to be important natural salinity removal mechanisms. Finally, loss of calcium, relative to monovalent cations, may decrease water quality for irrigation purposes through increasing the sodium adsorption ratio (SAR), despite a pross decrease in the TDS. The potential role of various reservoir operation options in managing natural salinity removal processes and the value of such removal is discussed

Aging in the Relaxor Ferroelectric PMN/PT

The relaxor ferroelectric (PbMn$_{1/3}$Nb$_{2/3}$O$_3$)$_{1-x}$(PbTiO$_3$)$_{x}$, $x=0.1$, (PMN/PT(90/10)) is found to exhibit several regimes of complicated aging behavior. Just below the susceptibility peak there is a regime exhibiting rejuvenation but little memory. At lower temperature, there is a regime with mainly cumulative aging, expected for simple domain-growth. At still lower temperature, there is a regime with both rejuvenation and memory, reminiscent of spin glasses. PMN/PT (88/12) is also found to exhibit some of these aging regimes. This qualitative aging behavior is reminiscent of that seen in reentrant ferromagnets, which exhibit a crossover from a domain-growth ferromagnetic regime into a reentrant spin glass regime at lower temperatures. These striking parallels suggest a picture of competition in PMN/PT (90/10) between ferroelectric correlations formed in the domain-growth regime with glassy correlations formed in the spin glass regime. PMN/PT (90/10) is also found to exhibit frequency-aging time scaling of the time-dependent part of the out-of-phase susceptibility for temperatures 260 K and below. The stability of aging effects to thermal cycles and field perturbations is also reported.Comment: 8 pages RevTeX4, 11 figures; submitted to Phys. Rev.

Extending Feynman's Formalisms for Modelling Human Joint Action Coordination

The recently developed Life-Space-Foam approach to goal-directed human action deals with individual actor dynamics. This paper applies the model to characterize the dynamics of co-action by two or more actors. This dynamics is modelled by: (i) a two-term joint action (including cognitive/motivatonal potential and kinetic energy), and (ii) its associated adaptive path integral, representing an infinite--dimensional neural network. Its feedback adaptation loop has been derived from Bernstein's concepts of sensory corrections loop in human motor control and Brooks' subsumption architectures in robotics. Potential applications of the proposed model in human--robot interaction research are discussed. Keywords: Psycho--physics, human joint action, path integralsComment: 6 pages, Late

Barkhausen Noise in a Relaxor Ferroelectric

Barkhausen noise, including both periodic and aperiodic components, is found in and near the relaxor regime of a familiar relaxor ferroelectric, PbMg$_{1/3}$Nb$_{2/3}$O$_3$, driven by a periodic electric field. The temperature dependences of both the amplitude and spectral form show that the size of the coherent dipole moment changes shrink as the relaxor regime is entered, contrary to expectations based on some simple models.Comment: 4 pages RevTeX4, 5 figures; submitted to Phys Rev Let