Related papers: Output-input coupling in thermally fluctuating bio…
Spontaneous symmetry breaking is a hallmark of equilibrium systems, typically characterized by a single critical point separating ordered and disordered phases. Recently, a novel class of non-equilibrium phase transitions was uncovered…
Comprehensive and predictive simulation of coupled reaction networks has long been a goal of biology and other fields. Currently, metabolic network models that utilize enzyme mass action kinetics have predictive power but are limited in…
With the formal construction of a thermodynamic spring, I describe the mechanics, energetics, entropy, and kinetics of a binary mechanical model system. A protein that transitions between two metastable structural states behaves as a…
We study the role of active coupling on the transport properties of homogeneously charged macromolecules in an infinitely dilute solution. An enzyme becomes actively bound to a segment of the macromolecule, exerting an electrostatic force…
Chemical reactions involve the movement of charges, and this work presents a mathematical model for describing chemical reactions in electrolytes. The model is developed using an energy variational method that aligns with classical…
Cytoskeletal motor proteins are involved in major intracellular transport processes which are vital for maintaining appropriate cellular function. The motor exhibits distinct states of motility: active motion along filaments, and…
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…
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…
Recently, strong coupling between non-Hermitian physical systems of different nature is widely investigated due to it endows them with new properties. In this work, we investigate the energy transport between strongly coupled systems. We…
Motor enzymes are remarkable molecular machines that use the energy derived from the hydrolysis of a nucleoside triphosphate to generate mechanical movement, achieved through different steps that constitute their kinetic cycle. These…
Cytoskeletal motors known as motor proteins are molecules that drive cellular transport along several parallel cytoskeletal filaments and support many biological processes. Experimental evidences suggest that they interact with the nearest…
The formation of condensates is now considered as a major organization principle of eukaryotic cells. Several studies have recently shown that the properties of these condensates are affected by enzymatic reactions. We propose here a simple…
Biological machines like molecular motors and enzymes operate in dynamic cycles representable as stochastic flows on networks. Current stochastic dynamics describes such flows on fixed networks. Here, we develop a scalable approach to…
We propose a general theory to describe the distribution of protein-folding transition paths. We show that transition paths follow a predictable sequence of high-free-energy transient states that are separated by free-energy barriers. Each…
We study a mechanism for reliable switching in biomolecular signal-transduction cascades. Steady bistable states are created by system-size cooperative effects in populations of proteins, in spite of the fact that the phosphorylation-state…
The metabolic processes complexity is at the heart of energy conversion in living organisms and forms a huge obstacle to develop tractable thermodynamic metabolism models. By raising our analysis to a higher level of abstraction, we develop…
The conformation space of a 20-residue antiparallel $\beta$-sheet peptide, sampled by molecular dynamics simulations, is mapped to a network. Conformations are nodes of the network, and the transitions between them are links. The…
The dynamics of stochastic reaction networks within cells are inevitably modulated by factors considered extrinsic to the network such as for instance the fluctuations in ribsome copy numbers for a gene regulatory network. While several…
Signal transduction within biological cells is governed by networks of interacting proteins. Communication between these proteins is mediated by signaling molecules which bind to receptors and induce stochastic transitions between different…
Protein machines often exhibit long range interplay between different sites in order to achieve their biological tasks. We investigate and characterize the non--linear energy localization and the basic mechanisms of energy transfer in…