A proposed delay line for hadron beams in RHIC

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Entropically driven transition to a liquid-crystalline polymer globule

A self-consistent-field theory (SCFT) in the grand canonical ensemble formulation is used to study transitions in a helix-coil multiblock copolymer globule. The helices are modeled as stiff rods. In addition to the established coil-globule transition we show for the first time that, even without explicit rod-rod alignment interaction, the system undergoes a transition to a nematic liquid-crystalline (LC) globular state. The LC-globule formation is driven by the hydrophobic helical segment attraction and the anisotropy of the globule surface energy. The full phase diagram of the copolymer was calculated. It discriminates between an open chain, amorphous globule and LC-globule. This model provides a relatively simple example of the interplay between secondary and tertiary structures in homopolypeptides. Moreover, it gives a simple explanation for the formation of helix bundles in certain globular proteins.Comment: 5 pages, 5 figures, submitted to Europhys. Let

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

Role of Secondary Motifs in Fast Folding Polymers: A Dynamical Variational Principle

A fascinating and open question challenging biochemistry, physics and even geometry is the presence of highly regular motifs such as alpha-helices in the folded state of biopolymers and proteins. Stimulating explanations ranging from chemical propensity to simple geometrical reasoning have been invoked to rationalize the existence of such secondary structures. We formulate a dynamical variational principle for selection in conformation space based on the requirement that the backbone of the native state of biologically viable polymers be rapidly accessible from the denatured state. The variational principle is shown to result in the emergence of helical order in compact structures.Comment: 4 pages, RevTex, 4 eps figure

Do Natural Proteins Differ from Random Sequences Polypeptides? Natural vs. Random Proteins Classification Using an Evolutionary Neural Network

Are extant proteins the exquisite result of natural selection or are they random sequences slightly edited by evolution? This question has puzzled biochemists for long time and several groups have addressed this issue comparing natural protein sequences to completely random ones coming to contradicting conclusions. Previous works in literature focused on the analysis of primary structure in an attempt to identify possible signature of evolutionary editing. Conversely, in this work we compare a set of 762 natural proteins with an average length of 70 amino acids and an equal number of completely random ones of comparable length on the basis of their structural features. We use an ad hoc Evolutionary Neural Network Algorithm (ENNA) in order to assess whether and to what extent natural proteins are edited from random polypeptides employing 11 different structure-related variables (i.e. net charge, volume, surface area, coil, alpha helix, beta sheet, percentage of coil, percentage of alpha helix, percentage of beta sheet, percentage of secondary structure and surface hydrophobicity). The ENNA algorithm is capable to correctly distinguish natural proteins from random ones with an accuracy of 94.36%. Furthermore, we study the structural features of 32 random polypeptides misclassified as natural ones to unveil any structural similarity to natural proteins. Results show that random proteins misclassified by the ENNA algorithm exhibit a significant fold similarity to portions or subdomains of extant proteins at atomic resolution. Altogether, our results suggest that natural proteins are significantly edited from random polypeptides and evolutionary editing can be readily detected analyzing structural features. Furthermore, we also show that the ENNA, employing simple structural descriptors, can predict whether a protein chain is natural or random

Self- generated disorder and structural glass formation in homopolymer globules

We have investigated the interrelation between the spin glasses and the structural glasses. Spin glasses in this case are random magnets without reflection symmetry (e.g. $p$ - spin interaction spin glasses and Potts glasses) which contain quenched disorder, whereas the structural glasses are here exemplified by the homopolymeric globule, which can be viewed as a liquid of connected molecules on nano scales. It is argued that the homopolymeric globule problem can be mapped onto a disorder field theoretical model whose effective Hamiltonian resembles the corresponding one for the spin glass model. In this sense the disorder in the globule is self - generated (in contrast to spin glasses) and can be related with competitive interactions (virial coefficients of different signs) and the chain connectivity. The work is aimed at giving a quantitative description of this analogy. We have investigated the phase diagram of the homopolymeric globule where the transition line from the liquid to glassy globule is treated in terms of the replica symmetry breaking paradigm. The configurational entropy temperature dependence is also discussed.Comment: 22 pages, 4 figures, submitted to Phys. Rev.

Reduction of beta* and increase of luminosity at RHIC

The reduction of {beta}* beyond the 1m design value at RHIC has been consistently achieved over the last 6 years of RHIC operations, resulting in an increase of luminosity for different running modes and species. During the recent 2007-08 deuteron-gold run the reduction to 0.70 from the design 1m achieved a 30% increase in delivered luminosity. The key ingredients allowing the reduction have been the capability of efficiently developing ramps with tune and coupling feedback, orbit corrections on the ramp, and collimation, to minimize beam losses in the final focus triplets, the main aperture limitations for the collision optics. We will describe the operational strategy used to reduce the {beta}*, at first squeezing the beam at store, to test feasibility, followed by the operationally preferred option of squeezing the beam during acceleration, and the resulting luminosity increase. We will conclude with future plans for the beta squeeze

Prerequisites for the creation of an atlas of postcovid inflammation as a way of personalized pharmacotherapy, as well as predicting and preventing organ and systemic dysfunctions

SARS-CoV-2 is a novel coronavirus that has been identified as the cause of the 2019 coronavirus infection (COVID-19), which originated at Wuhan city of PRC in late 2019 and widespread worldwide. As the number of patients recovering from COVID-19 continue to grow, it’s very important to understand what health issues they may keep experiencing. COVID-19 is now recognized as an infectious disease that can cause multiple organ diseases of various localization. It is against this background that a new term was introduced: post-acute post-COVID-19 syndrome characterized by several persistent symptoms inherent in the acute phase of the disease, as well as the occurrence of delayed and (or) long-term complications beyond 4 weeks from the onset of the disease. The work reflected in this article revealed a portrait of a patient with post-COVID-19 syndrome, the most common complications of this period, as well as the mechanisms of their development and the resulting metabolic, cellular, tissue disorders leading to the tissue and organ dysfunctions. A comprehensive biochemical and immunological screening was carried out using the example of three clinical cases to identify the most significant disorders in these patients and to correlate with their clinical status over time. In point of fact, such patients were diagnosed with vascular dysfunction factors (development of endothelial dysfunction), metabolic dysfunction factors (metabolic acidosis, mitochondrial dysfunction, carbohydrate metabolism disorder, insulin resistance, altered branched-chain and aromatic amino acid metabolism), neurological disorder factors (neurotoxicity of the resulting metabolites), immunological disorder factors (decreased efficiency of detoxification systems, secondary immunodeficiency, risk of secondary bacterial infection)