Mapping energy transport networks in proteins

The response of proteins to chemical reactions or impulsive excitation that occurs within the molecule has fascinated chemists for decades. In recent years ultrafast X-ray studies have provided ever more detailed information about the evolution of protein structural change following ligand photolysis, and time-resolved IR and Raman techniques, e.g., have provided detailed pictures of the nature and rate of energy transport in peptides and proteins, including recent advances in identifying transport through individual amino acids of several heme proteins. Computational tools to locate energy transport pathways in proteins have also been advancing. Energy transport pathways in proteins have since some time been identified by molecular dynamics (MD) simulations, and more recent efforts have focused on the development of coarse graining approaches, some of which have exploited analogies to thermal transport in other molecular materials. With the identification of pathways in proteins and protein complexes, network analysis has been applied to locate residues that control protein dynamics and possibly allostery, where chemical reactions at one binding site mediate reactions at distance sites of the protein. In this chapter we review approaches for locating computationally energy transport networks in proteins. We present background into energy and thermal transport in condensed phase and macromolecules that underlies the approaches we discuss before turning to a description of the approaches themselves. We also illustrate the application of the computational methods for locating energy transport networks and simulating energy dynamics in proteins with several examples

Colossal electroresistance and colossal magnetoresistive step in paramagnetic insulating phase of single crystalline bilayered manganite(La0.4_{0.4}Pr0.6_{0.6})1.2_{1.2}Sr1.8_{1.8}Mn2_{2}O7_{7}

We report a significant decrease in the low-temperature resistance induced by the application of an electric current on the $ab$-plane in the paramagnetic insulating (PMI) state of (La$_{0.4}$Pr$_{0.6}$)$_{1.2}$Sr$_{1.8}$Mn$_{2}$O$_{7}$. A colossal electroresistance effect attaining -95% is observed at lower temperatures. A colossal magnetoresistive step appears near 5T at low temperatures below 10K, accompanied by an ultrasharp width of the insulator-metal transition. Injection of higher currents to the crystal causes a disappearance of the steplike transition. These findings have a close relationship with the presence of the short-range charge-ordered clusters pinned within the PMI matrix of the crystal studied.Comment: 4 pages 3 figure

Steplike Lattice Deformation of Single Crystalline (La0.4_{0.4}Pr0.6_{0.6})1.2_{1.2}Sr1.8_{1.8}Mn2_{2}O7_{7} Bilayered Manganite

We report a steplike lattice transformation of single crystalline (La$_{0.4}$Pr$_{0.6}$)$_{1.2}$Sr$_{1.8}$Mn$_{2}$O$_{7}$bilayered manganite accompanied by both magnetization and magnetoresistive jumps, and examine the ultrasharp nature of the field-induced first-order transition from a paramagnetic insulator to a ferromagnetic metal phase accompanied by a huge decrease in resistance. Our findings support that the abrupt magnetostriction is closely related to an orbital frustration existing in the inhomogeneous paramagnetic insulating phase rather than a martensitic scenario between competing two phases.Comment: 5 pages,4figures, v4: figures are changed, in press in Phys.Rev.Let

Dwarf males in the barnacle Alepas pacifica Pilsbry, 1907 (Thoracica, Lepadidae), a symbiont of jellyfish

In the pedunculate barnacle Alepas pacifica Pilsbry, 1907, a symbiont of jellyfish, several small individuals were found attached to conspecifics rather than directly to the host. We investigated whether these individuals act as dwarf males, as is known in some other species of barnacles. The conspecific-attached individuals had longer penes than juvenile hermaphrodites of similar sizes attached directly to the jellyfish, although there was no other morphological difference between these two types of individuals. Only the largest conspecific-attached individual was ovigerous. We conclude that the conspecific-attached individuals are dwarf males, which develop the male function at a smaller size than hermaphrodites do, with a small possibility of becoming hermaphroditic. This is the first report of dwarf males, and hence of the coexistence of males and hermaphrodites (androdioecy), in the family Lepadidae. In addition, the record of A. pacifica attached to Nemopilema nomurai Kishinouye, 1922, is reported herein as new to science

Statistical Mechanics of the Chinese Restaurant Process: lack of self-averaging, anomalous finite-size effects and condensation

The Pitman-Yor, or Chinese Restaurant Process, is a stochastic process that generates distributions following a power-law with exponents lower than two, as found in a numerous physical, biological, technological and social systems. We discuss its rich behavior with the tools and viewpoint of statistical mechanics. We show that this process invariably gives rise to a condensation, i.e. a distribution dominated by a finite number of classes. We also evaluate thoroughly the finite-size effects, finding that the lack of stationary state and self-averaging of the process creates realization-dependent cutoffs and behavior of the distributions with no equivalent in other statistical mechanical models.Comment: (5pages, 1 figure

Perancangan Sistem Otomatisasi Dan Monitoring Bak Sampah Berbasis Internet Of Things (Iot)

Saat ini ada berbagai macam permasalahan dalam hal kebersihan lingkungan, misalnya bak sampah yang berlokasi ditaman sudah penuh namun belum juga dibesihkan petugas kebersihan. Adanya IoT memungkinkan dibangunnya sebuah sistem monitoring tempat sampah jarak jauh sehingga tidak aka nada lagi tempat sampah yang tidak kunjung dikosongkan. Sistem monitoring ini dirancang menggunakan Modul IoT Node MCU sebagai otak dari alat yang dirancang dengan menggunakan 2 sensor ultrasonik dengan fungsi yang berbeda dan 1 motor servo sebagai penggerak. Pada saat alat beroperasi, sensor ultrasonik 1 yang berfungsi mendeteksi jarak untuk membuka tutup bak sampah dengan jarak yang sudah ditentukan yaitu objek yang berada <50 cm dari sensor yang berada di depan bak sampah, jika objek berada >50 cm dari sensor yang berada di depan bak sampah maka tutup bak sampah tidak terbuka dan sensor ultrasonik 2 yang berada di dalam tutup bak sampah yang berfungsi untuk mendeteksi volume sampah

Surgical anatomy of the sural nerve for peripheral nerve reconstruction research in swine

The use of peripheral nerves as donor nerves for peripheral nerve regeneration studies, which can provide a long peripheral nerve with intact physiological functions, for autologous nerve grafts was unknown in swine. This study investigated the surgical anatomy of sural nerves (nervus suralis) of cadavers and anesthetized miniature pigs. A loose-S shape incision line was made from the border of the biceps femoris muscle (musculus biceps femoris) to 2 cm above the calx in the leg of anesthetized miniature pigs. The sural nerve was found to branch from the sciatic nerve (nervus ischiadicus) under the biceps femoris muscle and run along the small saphenous vein (vena saphena parva). After being isolated and stimulated using a nerve stimulator, the sural nerve innervated no muscles and tissues in the leg. The sural nerve (14.

Afadin requirement for cytokine expressions in keratinocytes during chemically induced inflammation in mice

Afadin is a filamentous actin-binding protein and a mediator of nectin signaling. Nectins are Ig-like cell adhesion molecules, and the nectin family is composed of four members, nectin-1 to nectin-4. Nectins show homophilic and heterophilic interactions with other nectins or proteins on adjacent cells. Nectin signaling induces formation of cell-cell junctions and is required for the development of epithelial tissues, including skin. This study investigated the role of afadin in epithelial tissue development and established epithelium-specific afadin-deficient (CKO) mice. Although showing no obvious abnormality in the skin development and homeostasis, the mice showed the reduced neutrophil infiltration into the epidermis during chemical-induced inflammation with 12-O-tetradecanoylphorbol 13-acetate (TPA). Immunohistochemical and quantitative real-time PCR analyses showed that the expression levels of cytokines including Cxcl2, Il-1{beta} and Tnf-{alpha} were reduced in CKO keratinocytes compared with control keratinocytes during TPA-induced inflammation. Primary-cultured skin keratinocytes from CKO mice also showed reduced expression of these cytokines and weak activation of Rap1 compared with those from control mice after the TPA treatment. These results suggested a remarkable function of afadin, which was able to enhance cytokine expression through Rap1 activation in keratinocytes during inflammation

Development and characterization of osteogenic cell sheets in an in vivo model

[Excerpt] Despite some successes in the tissue engineering field its evolution seems to be tampered by limitations such as cell sourcing and the lack of adequate scaffolds to support cell growth and differentiation. The use of stem cells combined with cell sheet engineering technology seems a promising way to overcome these limitations. In this work bone marrow cells were flushed from 3 weeks old Wistar rat femurs and cultured in basal DMEM medium until subconfluence. Cells were then transferred to thermo-responsive dishes (3 x10⁵ cells/dish) and cultured for 3 weeks in osteogenic medium. [...]info:eu-repo/semantics/publishedVersio