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Ubiquinone is an important component of the electron transfer chains in proteobacteria and eukaryotes. The biosynthesis of ubiquinone requires multiple steps, most of which are common to bacteria and eukaryotes. Whereas the enzymes of the…

Biomolecules · Quantitative Biology 2020-05-04 Sophie Saphia Abby , Katayoun Kazemzadeh , Charles Vragniau , Ludovic Pelosi , Fabien Pierrel

Eukaryotes tune the transcriptional activity of their genome by altering the nucleosome core particle through multiple chemical processes. In particular, replacement of the canonical H2A histone with the variants macroH2A and H2A.Z has been…

Biological Physics · Physics 2016-04-20 Samuel Bowerman , Jeff Wereszczynski

Muscle uses Ca2+ as a messenger to control contraction and relies on ATP to maintain the intracellular Ca2+ homeostasis. Mitochondria are the major sub-cellular organelle of ATP production. With a negative inner membrane potential,…

Biomolecules · Quantitative Biology 2016-07-29 Jingsong Zhou , Kamal Dhakal , Jianxun Yi

Rate theory and DFT calculations of hydrogen evolution reaction (HER) on MoS2 with Co, Ni and Pt impurities show the significance of dihydrogen (H2*) complex where both hydrogen atoms are interacting with the surface. Stabilization of such…

Materials Science · Physics 2024-09-05 Sander Ø. Hanslin , Hannes Jónsson , Jaakko Akola

Photosynthesis, the process by which energy from sunlight drives cellular metabolism, relies on a unique organization of light-harvesting and reaction center complexes. Recently, the organization of light-harvesting LH2 complexes and…

Biological Physics · Physics 2011-11-02 Elad Harel

Cellular cortex, which is a highly viscous thin cytoplasmic layer just below the cell membrane, controls the cell's mechanical properties, which can be characterized by a hydrodynamic length scale $\ell$. Cells actively regulate $\ell$ via…

Biological Physics · Physics 2018-06-08 Saroj Kumar Nandi

Cell-to-cell heterogeneity drives a range of (patho)physiologically important phenomena, such as cell fate and chemotherapeutic resistance. The role of metabolism, and particularly mitochondria, is increasingly being recognised as an…

Subcellular Processes · Quantitative Biology 2019-02-11 Juvid Aryaman , Iain G. Johnston , Nick S. Jones

The Cassini mission to the Saturn system discovered a plume of ice grains and water vapor erupting from cracks on the icy surface of the satellite Enceladus. This moon has a global ocean in contact with a rocky core beneath its icy…

Earth and Planetary Astrophysics · Physics 2020-12-17 Christine Ray , Christopher R. Glein , J. Hunter Waite , Ben Teolis , Tori Hoehler , Julie A. Huber , Jonathan Lunine , Frank Postberg

Photosynthetic microbes have evolved and successfully adapted to the ever-changing environmental conditions in complex microhabitats throughout almost all ecosystems on Earth. In the absence of light, they can sustain their biological…

Biological Physics · Physics 2024-07-16 Alexandros A. Fragkopoulos , Florian Böhme , Nicole Drewes , Oliver Bäumchen

Cellular metabolism, the integrated interconversion of thousands of metabolic substrates through enzyme-catalyzed biochemical reactions, is the most investigated complex intercellular web of molecular interactions. While the topological…

Molecular Networks · Quantitative Biology 2015-06-26 E. Almaas , B. Kovacs , T. Vicsek , Z. N. Oltvai , A. -L. Barabasi

The cytoplasm and biomembranes in biological cells contain large numbers of proteins that cyclically change their shapes. They are molecular machines that can function as molecular motors or carry out many other tasks in the cell. We…

Soft Condensed Matter · Physics 2016-02-17 Alexander Mikhailov , Raymond Kapral

Enhanced dynamical fluctuations of RNAs, facilitated by a network of water molecules with strong interactions with RNA, are suspected to be critical in their ability to respond to a variety of cellular signals. Using atomically detailed…

Biomolecules · Quantitative Biology 2015-01-15 Jeseong Yoon , Jong-Chin Lin , Changbong Hyeon , D. Thirumalai

Metabolism displays striking and robust regularities in the forms of modularity and hierarchy, whose composition may be compactly described. This renders metabolic architecture comprehensible as a system, and suggests the order in which…

Molecular Networks · Quantitative Biology 2015-06-05 Rogier Braakman , Eric Smith

Understanding how the collective physical processes drive robust morphological transitions in animal development requires the characterization of the relevant fields underlying morphogenesis. Calcium (Ca2+) is known to be such a field. Here…

Biological Physics · Physics 2023-04-26 Oded Agam , Erez Braun

Respiration in bacteria involves a sequence of energetically-coupled electron and proton transfers creating an electrochemical gradient of protons (a proton-motive force) across the inner bacterial membrane. With a simple kinetic model we…

Biological Physics · Physics 2015-05-13 Anatoly Yu. Smirnov , Sergey E. Savel'ev , Franco Nori

The more we learn about the cytoplasm of cells, the more we realise that the cytoplasm is not uniform but instead is highly inhomogeneous. In any inhomogeneous solution, there are concentration gradients, and particles move either up or…

Subcellular Processes · Quantitative Biology 2019-04-03 Richard P. Sear

The diffusional dynamics and vibrational spectroscopy of molecular hydrogen (H$_2$) in myoglobin (Mb) is characterized. Hydrogen has been implicated in a number of physiologically relevant processes, including cellular aging or…

Chemical Physics · Physics 2024-09-16 Jiri Käser , Kai Töpfer , Markus Meuwly

Heterostructures of 2D materials offer a fertile ground to study ion transport and charge storage. Here we employ ab initio molecular dynamics to examine the proton-transfer/diffusion and redox behavior in a water layer confined in the…

Chemical Physics · Physics 2022-01-12 Lihua Xu , De-en Jiang

A central and long-standing issue in evolutionary theory is the origin of the biological variation upon which natural selection acts1. Some hypotheses suggest that evolutionary change represents an adaptation to the surrounding environment…

Statistical Mechanics · Physics 2007-05-23 J. Podani , Z. N. Oltvai , H. Jeong , B. Tombor , A. -L. Barabasi , E. Szathmary

Found in all eukaryotic cells, linker histones H1 are known to bind to and rearrange nucleosomal linker DNA. In vitro, the fundamental nature of H1/DNA interactions has attracted wide interest among research communities - for biologists…

Biological Physics · Physics 2010-08-12 Rolf Dootz , Adriana Cristina Toma , Thomas Pfohl
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