Seismic Response Analysis of Forebay Structure for CW Pump House of a Nuclear Power Project

The paper reviews the current state-of-the-art on the seismic response analysis of complex RCC structure like forebay which is usually connected with CW Pump House frame at its rear end for fulfilling circulating water requirement in power plant - nuclear or thermal. The need to include in such analysis and design effects of 3-Dimensional mathematical model and soil-structure interaction for studying overall behaviour of the structure are highlighted. The paper also discusses the usefulness, if any, of such rigorous analysis and identifies some problem areas in finalising realistic design data and adopting suitable models to represent the structural system

Kinetics and Free Energy of Ligand Dissociation Using Weighted Ensemble Milestoning

We consider the recently developed weighted ensemble milestoning (WEM) scheme [J. Chem. Phys. 152, 234114 (2020)], and test its capability of simulating ligand-receptor dissociation dynamics. We performed WEM simulations on the following host-guest systems: Na$^+$/Cl$^-$ ion pair and 4-hydroxy-2-butanone (BUT) ligand with FK506 binding protein (FKBP). As proof or principle, we show that the WEM formalism reproduces the Na$^+$/Cl$^-$ ion pair dissociation timescale and the free energy profile obtained from long conventional MD simulation. To increase accuracy of WEM calculations applied to kinetics and thermodynamics in protein-ligand binding, we introduced a modified WEM scheme called weighted ensemble milestoning with restraint release (WEM-RR), which can increase the number of starting points per milestone without adding additional computational cost. WEM-RR calculations obtained a ligand residence time and binding free energy in agreement with experimental and previous computational results. Moreover, using the milestoning framework, the binding time and rate constants, dissociation constant and the committor probabilities could also be calculated at a low computational cost. We also present an analytical approach for estimating the association rate constant ($k_{\text{on}}$) when binding is primarily diffusion driven. We show that the WEM method can efficiently calculate multiple experimental observables describing ligand-receptor binding/unbinding and is a promising candidate for computer-aided inhibitor design

Vitamin D kao sastojak luminalne tekućine pasjemenika važan je za sazrijevanje spermija u nerasta pasmine veliki bijeli jorkšir

Vitamin-D (VD) is known to modulate reproductive processes through the expression of VDR in the male reproductive tract. To understand its influence in the initiation of sperm motility in epididymis, VD concentration was measured in serum, epididymal luminal fluid (ELF) and sperm cytosolic fluid (SCF) from the caput, corpus and cauda epididymis of Large White Yorkshire (LWY) boars (n = 30) of around 3-4 years of age. The relationship of VD concentration with sperm motility in epididymal segments was then observed. A progressive increase in sperm motility from caput to cauda epididymis was found with highest in cauda followed by corpus. Motility was found absent in the caput region. VD levels in serum were positively correlated with spermatozoan motility from the corpus (r = 0.819) and cauda (r = 0.961), and this was highly significant (P0.05) from sections of caput to cauda epididymis was in concurrence with the increasing concentration of VD from the caput to cauda epididymis suggesting the influence of VD in the initiation of sperm motility in the excurrent duct. VD levels in serum may also pave the way for the development of specific marker(s) to assist in the prediction and early diagnosis of idiopathic infertility in males due to epididymal dysfunction resulting from VD deficiency. This will help clinically in improving treatment modalities of this idiopathic male infertility.vu mužjaka. Kako bismo razumjeli njegov utjecaj na pokretanje spermija u pasjemeniku, izmjerena je koncentracija vitamina D u serumu, luminalnoj tekućini pasjemenika (ELF) i citosolnoj tekućini spermija (SCF) uzetoj iz glave, tijela i repa pasjemenika nerasta pasmine veliki bijeli jorkšir (n = 30) dobi 3 - 4 godine. Promatran je odnos koncentracije vitamina D i pokretljivosti spermija u dijelovima pasjemenika. Uočeno je progresivno povećanje pokretljivosti spermija od glave (gdje su mirovali) preko tijela do repa pasjemenika. Razine vitamina D u serumu pozitivno su korelirale s pokretljivošću spermija iz tijela (r = 0,819) i repa (r = 0,961), što je bilo statistički znakovito (P0,05) iz dijelova od glave do repa pasjemenika porasla je istodobno s porastom koncentracije vitamina D što upućuje na utjecaj vitamina D na početak pokretljivosti spermija u odvodnim kanalima. Razine vitamina D u serumu mogle bi utrti put razvoju specifičnih markera koji bi mogli pomoći u ranom dijagnosticiranju idiopatske neplodnosti u mužjaka uzrokovane disfunkcijom pasjemenika zbog manjka vitamina D. To može klinički pomoći u unapređenju modaliteta liječenja idiopatske neplodnosti u mužjaka

Rare Event Kinetics from Adaptive Bias Enhanced Sampling

We introduce a novel enhanced sampling approach named OPES flooding for calculating the kinetics of rare events from atomistic molecular dynamics simulation. This method is derived from the On-the-fly-Probability-Enhanced-Sampling (OPES) approach [Invernizzi and Parrinello, JPC Lett. 2020], which has been recently developed for calculating converged free energy surfaces for complex systems. In this paper, we describe the theoretical details of the OPES flooding technique and demonstrate the application on three systems of increasing complexity: barrier crossing in a two-dimensional double well potential, conformational transition in the alanine dipeptide in gas phase, and the folding and unfolding of the chignolin polypeptide in aqueous environment. From extensive tests, we show that the calculation of accurate kinetics not only requires the transition state to be bias-free, but the amount of bias deposited should also not exceed the effective barrier height measured along the chosen collective variables. In this vein, the possibility of computing rates from biasing suboptimal order parameters has also been explored. Furthermore, we describe the choice of optimum parameter combinations for obtaining accurate results from limited computational effort

Astrophysical S_{17}(0) factor from a measurement of d(7Be,8B)n reaction at E_{c.m.} = 4.5 MeV

Angular distribution measurements of $^2$H($^7$Be,$^7$Be)$^2$H and $^2$H($^7$Be,$^8$B)$n$ reactions at $E_{c.m.}\sim$~4.5 MeV were performed to extract the astrophysical $S_{17}(0)$ factor using the asymptotic normalization coefficient (ANC) method. For this purpose a pure, low emittance $^7$Be beam was separated from the primary $^7$Li beam by a recoil mass spectrometer operated in a novel mode. A beam stopper at 0$^{\circ}$ allowed the use of a higher $^7$Be beam intensity. Measurement of the elastic scattering in the entrance channel using kinematic coincidence, facilitated the determination of the optical model parameters needed for the analysis of the transfer data. The present measurement significantly reduces errors in the extracted $^7$Be(p,$\gamma$) cross section using the ANC method. We get $S_{17}$~(0)~=~20.7~$\pm$~2.4 eV~b.Comment: 15 pages including 3 eps figures, one figure removed and discussions updated. Version to appear in Physical Review

Optimization of relativistic mean field model for finite nuclei to neutron star matter

We have optimized the parameters of extended relativistic mean-field model using a selected set of global observables which includes binding energies and charge radii for nuclei along several isotopic and isotonic chains and the iso-scalar giant monopole resonance energies for the $^{90}$Zr and $^{208}$Pb nuclei. The model parameters are further constrained by the available informations on the energy per neutron for the dilute neutron matter and bounds on the equations of state of the symmetric and asymmetric nuclear matter at supra-nuclear densities. Two new parameter sets BSP and IUFSU* are obtained, later one being the variant of recently proposed IUFSU parameter set. The BSP parametrization uses the contributions from the quartic order cross-coupling between $\omega$ and $\sigma$ mesons to model the high density behaviour of the equation of state instead of the $\omega$ meson self-coupling as in the case of IUFSU* or IUFSU. Our parameter sets yield appreciable improvements in the binding energy systematics and the equation of state for the dilute neutron matter. The importance of the quartic order $\omega-\sigma$ cross coupling term of the extended RMF model, as often ignored, is realized.Comment: 22 pages, 11 figures, Nucl. Phys. A (in press

Cell death and infection: A double-edged sword for host and pathogen survival

Host cell death is an intrinsic immune defense mechanism in response to microbial infection. However, bacterial pathogens use many strategies to manipulate the host cell death and survival pathways to enhance their replication and survival. This manipulation is quite intricate, with pathogens often suppressing cell death to allow replication and then promoting it for dissemination. Frequently, these effects are exerted through modulation of the mitochondrial pro-death, NF-κB–dependent pro-survival, and inflammasome-dependent host cell death pathways during infection. Understanding the molecular details by which bacterial pathogens manipulate cell death pathways will provide insight into new therapeutic approaches to control infection

Guidelines for the use and interpretation of assays for monitoring autophagy (4th edition)1.

In 2008, we published the first set of guidelines for standardizing research in autophagy. Since then, this topic has received increasing attention, and many scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Thus, it is important to formulate on a regular basis updated guidelines for monitoring autophagy in different organisms. Despite numerous reviews, there continues to be confusion regarding acceptable methods to evaluate autophagy, especially in multicellular eukaryotes. Here, we present a set of guidelines for investigators to select and interpret methods to examine autophagy and related processes, and for reviewers to provide realistic and reasonable critiques of reports that are focused on these processes. These guidelines are not meant to be a dogmatic set of rules, because the appropriateness of any assay largely depends on the question being asked and the system being used. Moreover, no individual assay is perfect for every situation, calling for the use of multiple techniques to properly monitor autophagy in each experimental setting. Finally, several core components of the autophagy machinery have been implicated in distinct autophagic processes (canonical and noncanonical autophagy), implying that genetic approaches to block autophagy should rely on targeting two or more autophagy-related genes that ideally participate in distinct steps of the pathway. Along similar lines, because multiple proteins involved in autophagy also regulate other cellular pathways including apoptosis, not all of them can be used as a specific marker for bona fide autophagic responses. Here, we critically discuss current methods of assessing autophagy and the information they can, or cannot, provide. Our ultimate goal is to encourage intellectual and technical innovation in the field