Inferring the Rate-Length Law of Protein Folding

We investigate the rate-length scaling law of protein folding, a key undetermined scaling law in the analytical theory of protein folding. We demonstrate that chain length is a dominant factor determining folding times, and that the unambiguous determination of the way chain length corre- lates with folding times could provide key mechanistic insight into the folding process. Four specific proposed laws (power law, exponential, and two stretched exponentials) are tested against one an- other, and it is found that the power law best explains the data. At the same time, the fit power law results in rates that are very fast, nearly unreasonably so in a biological context. We show that any of the proposed forms are viable, conclude that more data is necessary to unequivocally infer the rate-length law, and that such data could be obtained through a small number of protein folding experiments on large protein domains

Is Heteropolymer Freezing Well Described by the Random Energy Model?

It is widely held that the Random Energy Model (REM) describes the freezing transition of a variety of types of heteropolymers. We demonstrate that the hallmark property of REM, statistical independence of the energies of states over disorder, is violated in different ways for models commonly employed in heteropolymer freezing studies. The implications for proteins are also discussed.Comment: 4 pages, 3 eps figures To appear in Physical Review Letters, May 199

Freezing Transition of Random Heteropolymers Consisting of an Arbitrary Set of Monomers

Mean field replica theory is employed to analyze the freezing transition of random heteropolymers comprised of an arbitrary number ($q$) of types of monomers. Our formalism assumes that interactions are short range and heterogeneity comes only from pairwise interactions, which are defined by an arbitrary $q \times q$ matrix. We show that, in general, there exists a freezing transition from a random globule, in which the thermodynamic equilibrium is comprised of an essentially infinite number polymer conformations, to a frozen globule, in which equilibrium ensemble is dominated by one or very few conformations. We also examine some special cases of interaction matrices to analyze the relationship between the freezing transition and the nature of interactions involved.Comment: 30 pages, 1 postscript figur

An approach to interstitial lung disease in India

Interstitial lung diseases are common and have varied etiology, clinical presentation, clinical course and outcome. They pose a diagnostic challenge to physicians and pulmonologists. Patients present with dry cough, exertional dyspnoea, interstitial lesions on X-ray of the chest and restrictive ventilatory defect on spirometry. A sharp decline in oxygen saturation with exercise is characteristic. Careful evaluation of the history of the patient and physical examination help in narrowing down diagnostic probabilities. HRCT of the chest has emerged as an important tool in the evaluation of these disorders. Idiopathic Interstitial Pneumonias (IIP) are a group of conditions which are classified into several types based on pathological features. Bronchoscopic procedures are helpful in diagnosis of certain disorders but are of limited value in classification of IIP which requires surgical biopsy. Usual Interstitial Pneumonia (UIP), also referred to as Idiopathic Pulmonary Fibrosis, has a progressive course and an unfavourable outcome. Certain new drugs have recently become available for treatment of UIP. Our approach towards diagnosis and management of interstitial lung diseases based on personal experience over the past three decades is reported here. Key words: Usual interstitial pneumonia – sarcoidosis – pneumoconiosis – bronchoscopy – lung biopsyÂ

Influence of clipping and water stress on growth performance and nutrient value of four range grasses

The paper examines the effect of water stress and clipping treatments on growth behaviour and nutrient value of 4 grasses, viz.,Lolium perenne, Poa pratensis (both C3 plants), Chloris gayana and Panicum coloratum (both C4 plants). Biomass, net production, relative growth rates were affected more markedly and adversely in the two C4 species due to water stress. The effect of clipping varied with species and was generally more marked and adverse in two C4 species. The C3 plants developed higher R:S ratio under water stress. Water stress resulted in a greater decline of total non-structural carbohydrate and protein content in the two Q species. Clipping affected adversely the non-structural carbohydrate content and again the effect was more marked in the two C4species. On the other hand, protein content in shoots of all plants increased due to clipping

Gunrock: A High-Performance Graph Processing Library on the GPU

For large-scale graph analytics on the GPU, the irregularity of data access and control flow, and the complexity of programming GPUs have been two significant challenges for developing a programmable high-performance graph library. "Gunrock", our graph-processing system designed specifically for the GPU, uses a high-level, bulk-synchronous, data-centric abstraction focused on operations on a vertex or edge frontier. Gunrock achieves a balance between performance and expressiveness by coupling high performance GPU computing primitives and optimization strategies with a high-level programming model that allows programmers to quickly develop new graph primitives with small code size and minimal GPU programming knowledge. We evaluate Gunrock on five key graph primitives and show that Gunrock has on average at least an order of magnitude speedup over Boost and PowerGraph, comparable performance to the fastest GPU hardwired primitives, and better performance than any other GPU high-level graph library.Comment: 14 pages, accepted by PPoPP'16 (removed the text repetition in the previous version v5

Free Energy Self-Averaging in Protein-Sized Random Heteropolymers

Current theories of heteropolymers are inherently macrpscopic, but are applied to folding proteins which are only mesoscopic. In these theories, one computes the averaged free energy over sequences, always assuming that it is self-averaging -- a property well-established only if a system with quenched disorder is macroscopic. By enumerating the states and energies of compact 18, 27, and 36mers on a simplified lattice model with an ensemble of random sequences, we test the validity of the self-averaging approximation. We find that fluctuations in the free energy between sequences are weak, and that self-averaging is a valid approximation at the length scale of real proteins. These results validate certain sequence design methods which can exponentially speed up computational design and greatly simplify experimental realizations.Comment: 4 pages, 3 figure

Housing and Mobility Toolkit for San Mateo County

Since the end of the Great Recession, San Mateo County has attracted new workers at a record rate without building anywhere near enough housing. This jobs-housing imbalance drives the cost of housing up and forces many moderate and lower-income employees and their families out of the County. A lack of access to quality affordable housing in the County and the entire Bay Area along with limited transportation options means that an increased number of employees drive in and out of the County every workday. The resultant congestion, gridlock, and long commutes along with other negative environmental, social, and economic impacts create a major concern for communities in the County and beyond. Clearly, this problem has two distinct but interrelated dimensions: housing development and transportation planning. A select group of Mineta Transportation Institute (MTI) Research Associates worked closely with representatives from the San Mateo County Home for All initiative to help address this challenge by developing a toolkit of successful case studies with a holistic approach to housing development and transportation planning