Related papers: ATP synthase: evolution, energetics, and membrane …
Liquid-liquid phase separation of aqueous two-phase system (ATPS) is fundamental across physical and biological sciences. While well understood for passive systems, how this process is regulated by active agents such as motile bacteria…
The Na$^+$/K$^+$ ATPase is an essential component of cardiac electrophysiology, maintaining physiological Na$^+$ and K$^+$ concentrations over successive heart beats. Terkildsen et al. (2007) developed a model of the ventricular myocyte…
Polymerases are protein enzymes that move along nucleic acid chains and catalyze template-based polymerization reactions during gene transcription and replication. The polymerases also substantially improve transcription or replication…
Cells generally convert nutrient resources to useful products via energy transduction. Accordingly, the thermodynamic efficiency of this conversion process is one of the most essential characteristics of living organisms. However, although…
Cytoskeletal motor proteins move on filamentous tracks by converting input chemical energy that they derive by catalyzing the hydrolysis of ATP. The ATPase site is the analog of an engine and hydrolysis of ATP is the analog of burning of…
A polarizable environment, prominently the solvent, responds to electronic changes in biomolecules rapidly. The knowledge of conformational relaxation of the biomolecule itself, however, may be scarce or missing. In this work, we describe…
F1-ATPase (or F1), the highly-efficient and reversible biochemical engine, has motivated physicists as well as biologists to imagine the design principles governing machines in the fluctuating world. Recent experiments have clarified yet…
Nonequilibrium dynamics of biomembranes with active inclusions is considered. The inclusions represent protein molecules which perform cyclic internal conformational motions driven by the energy brought with ATP ligands. As protein…
The cytoskeletal component actomyosin is a canonical example of active matter since the powerstroke cycle locally converts chemical energy in the form of adenoside triphosphate (ATP) into mechanical work for remodelling. Observing myosin II…
FoF1-ATP synthase catalyzes the synthesis of adenosine triphosphate (ATP). The F1 portion can be stripped from the membrane-embedded Fo portion of the enzyme. F1 acts as an ATP hydrolyzing enzyme, and ATP hydrolysis is associated with…
Filament formation by non-cytoskeletal enzymes has been known for decades, yet only relatively recently has its wide-spread role in enzyme regulation and biology come to be appreciated. This comprehensive review summarizes what is known for…
Nature, a synthetic master, creates more than 300,000 natural products (NPs) which are the major constituents of FDA-proved drugs owing to the vast chemical space of NPs. To date, there are fewer than 30,000 validated NPs compounds involved…
Using data from gene expression databases on various organisms and tissues, including yeast, nematodes, human normal and cancer tissues, and embryonic stem cells, we found that the abundances of expressed genes exhibit a power-law…
This review discusses research developments and applications of isotachophoresis (ITP) to the initiation, control, and acceleration of chemical reactions, emphasizing reactions involving biomolecular reactants such as nucleic acids,…
Photosynthetic life requires sufficient photosynthetically active radiation (PAR) to metabolise. On Earth, plant behaviour, physiology and metabolism are sculpted around the night-day cycle by an endogenous biological circadian clock. The…
Collective dynamics and force generation by cytoskeletal filaments are crucial in many cellular processes. Investigating growth dynamics of a bundle of N independent cytoskeletal filaments pushing against a wall, we show that chemical…
The ribosome is one of the largest and most complex macromolecular machines in living cells. It polymerizes a protein in a step-by-step manner as directed by the corresponding nucleotide sequence on the template messenger RNA (mRNA) and…
Even when concepts similar to emergence have been used since antiquity, we lack an agreed definition. However, emergence has been identified as one of the main features of complex systems. Most would agree on the statement ``life is…
We describe a concept that has the potential to change how we think about the underlying mechanisms of cell membrane electroporation (EP). Prior experimental, theoretical and modeling have emphasized a single pore lifetime as adequate for…
We present a thermodynamically consistent energetic variational model for active nematics driven by ATP hydrolysis, with a focus on the coupling between chemical reactions and mechanical dynamics. Extending the classical Toner-Tu framework,…