Atomic-scale characterization of mature HIV-1 capsid stabilization by inositol hexakisphosphate (IP₆)

Inositol hexakisphosphates (IP6) are cellular cofactors that promote the assembly of mature capsids of HIV. These negatively charged molecules coordinate an electropositive ring of arginines at the center of pores distributed throughout the capsid surface. Kinetic studies indicate that the binding of IP6 increases the stable lifetimes of the capsid by several orders of magnitude from minutes to hours. Using all-atom molecular dynamics simulations, we uncover the mechanisms that underlie the unusually high stability of mature capsids in complex with IP6. We find that capsid hexamers and pentamers have differential binding modes for IP6. Ligand density calculations show three sites of interaction with IP6 including at a known capsid inhibitor binding pocket. Free energy calculations demonstrate that IP6 preferentially stabilizes pentamers over hexamers to enhance fullerene modes of assembly. These results elucidate the molecular role of IP6 in stabilizing and assembling the retroviral capsid

Validity of the zero-thermodynamic law in off-equilibrium coupled harmonic oscillators

In order to describe the thermodynamics of the glassy systems it has been recently introduced an extra parameter also called effective temperature which generalizes the fluctuation-dissipation theorem (FDT) to systems off-equilibrium and supposedly describes thermal fluctuations around the aging state. Here we investigate the applicability of a zero-th law for non-equilibrium glassy systems based on these effective temperatures by studying two coupled subsystems of harmonic oscillators with Monte Carlo dynamics. We analyze in detail two types of dynamics: 1) sequential dynamics where the coupling between the subsystems comes only from the Hamiltonian and 2) parallel dynamics where there is a further coupling between the subsystems arising from the dynamics. We show that the coupling described in the first case is not enough to make asymptotically the effective temperatures of two interacting subsystems coincide, the reason being the too small thermal conductivity between them in the aging state. This explains why different interacting degrees of freedom in structural glasses may stay at different effective temperatures without never mutually thermalizing.Comment: 23 pages, REVTeX, 4 eps figure

Differential expression of PKD1 and PKD2 in gastric cancer and analysis of PKD1 and PKD2 function in the model system

Aim: To study the differential expression of PKD1 and PKD2 in primary gastric cancer samples and to examine the role of PKD1 and PKD2 protein kinases in regulation of gastric tumor cell biology in the model system. Methods: Tumor samples of different histological variants of primary gastric cancer were analyzed. PKD1 and PKD2 expression levels in tumor samples were accessed by Western blot analysis and quantitative polymerase chain reaction (Q-PCR). As a model system we have used gastric adenocarcinoma сell line AGS sublines constitutively transfected by pcDNA3.1 coding PKD1 or PKD2, or empty pcDNA3.1 vector. These cell lines were analyzed by Western blot, Q-PCR, MTT and proliferation assays, in vitro scratch and Transwell assays, clonogenic assay. Results: It was found that primary gastric tumors possess different levels of PKD1 and PKD2 expression on mRNA and protein levels. Low level of PKD1 expression on protein and mRNA level was detected in low differentiated adenocarcinoma and ring cell gastric cancer — disorders with poor clinical prognosis. The high level of PKD2 expression was also found in gastric tumors with poor prognosis: low differentiated adenocarcinoma and adenogen cancer. To find out whether differential expression of PKD1 and PKD2 could affect biology of gastric tumor cells in vitro, we used a model system based on AGS cell line that constitutively expressed PKD1 or overexpressed PKD2. PKD1 transfection led to the inhibition of cell proliferation, migration and colony formation, in the meanwhile, the PKD2 overexpression enhanced proliferation, migration and colony formation capacities of AGS cells. Conclusions: Our data suggest that both downregulation of PKD1 or upregulation of PKD2 expression may determine the behavior of gastric tumor cells, which promotes invasive phenotype and could result in general poor prognosis

A Comparative Study of fBf_B within QCD Sum Rules with Two Typical Correlators up to Next-to-Leading Order

The B-decay constant $f_B$ is an important component for studying $B$-meson decays, which can be studied through QCD sum rules. We make a detailed discussion on $f_B$ from two sum rules, i.e. sum rules I and II, which are derived from the conventional correlator and the correlator with chiral currents respectively. It is found that these two sum rules are consistent with each other. However, the sum rules II has less uncertainty sources than that of sum rules I, and then it can be more accurate if we know the dimension-four gluon condensate well. It is found that $f_B$ decreases with the increment of $m_b$, and to compare with the Belle experimental data on $f_B$, both sum rules prefer smaller pole $b$-quark mass, $m_b=4.68\pm0.07$ GeV. By varying all the input parameters in their reasonable region and adding all the uncertainties together in quadrature, we obtain $f_B=172^{+23}_{-25}$ MeV for sum rules I and $f_B=214_{-34}^{+26}$ MeV for sum rules II.Comment: 11 pages, 4 figures, 2 tables. To match the printed version. To be published in Communications in Theoretical Physic

A tunable radiation source by coupling laser-plasma-generated electrons to a periodic structure

Near-infrared radiation around 1000 nm generated from the interaction of a high-density MeV electron beam, obtained by impinging an intense ultrashort laser pulse on a solid target, with a metal grating is observed experimentally. Theoretical modeling and particle-in-cell simulation suggest that the radiation is caused by the Smith-Purcell mechanism. The results here indicate that tunable terahertz radiation with tens GV=m field strength can be achieved by using appropriate grating parameter

Analysis of Newtonian heating and higher-order chemical reaction on a Maxwell nanofluid in a rotating frame with gyrotactic microorganisms and variable heat source/sink

The goal of this study is to investigate the rotating Maxwell nanoliquid flow incorporating gyrotactic microbes with Newtonian heating and irregular heat source sink. The motion of the flow is induced due to linearly unidirectional elongated surface. The uniqueness of the flow is enhanced by the inclusion of additional phenomenon of higher order chemical reaction incorporated with Darcy Forchheimer flow, Fourier and Fick law. Numerical solution of the formulated problem is developed via bvp4c function in MATLAB. The influence of the embroiled parameters on the flow distribution is demonstrated through various graphs and tables. It is noticed that fluid velocity declines on incrementing the rotation parameter. An upsurge in thermal field is portrayed on augmenting the Newtonian heating. Comparative analysis of the results of the proposed model with previous published research is included which confirms the validity of the current model

Privacy Architectures: Reasoning About Data Minimisation and Integrity

Privacy by design will become a legal obligation in the European Community if the Data Protection Regulation eventually gets adopted. However, taking into account privacy requirements in the design of a system is a challenging task. We propose an approach based on the specification of privacy architectures and focus on a key aspect of privacy, data minimisation, and its tension with integrity requirements. We illustrate our formal framework through a smart metering case study.Comment: appears in STM - 10th International Workshop on Security and Trust Management 8743 (2014

Innovative ligand-assisted synthesis of NIR-activated iron oxide for cancer theranostics

This work presents the development of a facile ligand-assisted hydrothermal reaction for the preparation of NIR-activated Fe3O4 nanostructures that can directly upgrade the iron oxide with MR contrast ability to be a MRI/photothermal theranostic agent

Theory of nonlinear optical properties of phenyl-substituted polyacetylenes

In this paper we present a theoretical study of the third-order nonlinear optical properties of poly(diphenyl)polyacetylene (PDPA) pertaining to the third-harmonic-generation (THG) process. We study the aforesaid process in PDPA's using both the independent electron Hueckel model, as well as correlated-electron Pariser-Parr-Pople (P-P-P) model. The P-P-P model based calculations were performed using various configuration interaction (CI) methods such as the the multi-reference-singles-doubles CI (MRSDCI), and the quadruples-CI (QCI) methods, and the both longitudinal and the transverse components of third-order susceptibilities were computed. The Hueckel model calculations were performed on oligo-PDPA's containing up to fifty repeat units, while correlated calculations were performed for oligomers containing up to ten unit cells. At all levels of theory, the material exhibits highly anisotropic nonlinear optical response, in keeping with its structural anisotropy. We argue that the aforesaid anisotropy can be divided over two natural energy scales: (a) the low-energy response is predominantly longitudinal and is qualitatively similar to that of polyenes, while (b) the high-energy response is mainly transverse, and is qualitatively similar to that of trans-stilbene.Comment: 13 pages, 7 figures (included), to appear in Physical Review B (April 15, 2004

Multiple (inverse) binomial sums of arbitrary weight and depth and the all-order epsilon-expansion of generalized hypergeometric functions with one half-integer value of parameter

We continue the study of the construction of analytical coefficients of the epsilon-expansion of hypergeometric functions and their connection with Feynman diagrams. In this paper, we show the following results: Theorem A: The multiple (inverse) binomial sums of arbitrary weight and depth (see Eq. (1.1)) are expressible in terms of Remiddi-Vermaseren functions. Theorem B: The epsilon expansion of a hypergeometric function with one half-integer value of parameter (see Eq. (1.2)) is expressible in terms of the harmonic polylogarithms of Remiddi and Vermaseren with coefficients that are ratios of polynomials. Some extra materials are available via the www at this http://theor.jinr.ru/~kalmykov/hypergeom/hyper.htmlComment: 24 pages, latex with amsmath and JHEP3.cls; v2: some typos corrected and a few references added; v3: few references added