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Entropy generation in a chemical reaction is analyzed without using the general formalism of non-equilibrium thermodynamics at a level adequate for advanced undergraduates. In a first approach to the problem, the phenomenological kinetic…
Bacteria are ubiquitous in our daily lives, either as motile planktonic cells or as immobilized surface-attached biofilms. These different phenotypic states play key roles in agriculture, environment, industry, and medicine; hence, it is…
This is a short survey on recent results obtained by the authors on dynamical phase transitions of interacting particle systems. We consider particle systems with exclusion dynamics, but it is conjectured that our results should hold for a…
Fueled by the hydrolysis of ATP, the motor protein kinesin literally walks on two legs along the biopolymer microtubule. The number of accidental backsteps that kinesin takes appears to be much larger than what one would expect given the…
Biological nanomachines are nanometer-size macromolecular complexes that catalyze chemical reactions in the presence of substrate molecules. The catalytic functions carried out by such nanomachines in the cytoplasm, and biological membranes…
Biological molecular motors are high-performance nanomachines that convert chemical energy into mechanical motion via chemomechanical coupling. Their reaction cycles typically comprise a series of intermediate chemical states between the…
We assess heat and mass transfer limitations in in situ studies of model catalysts with a first-principles based multiscale modeling approach that integrates a detailed description of the surface reaction chemistry and the macro-scale flow…
Emergence and maintenance of excitability is often phrased in terms of arriving at and remaining about a manifold of 'solutions' embedded in a high dimensional parameter space. Alongside studies that extend traditional focus on…
Cloud microphysical parameterizations in atmospheric models describe the formation and evolution of clouds and precipitation, a central weather and climate process. Cloud-associated latent heating is a primary driver of large and…
The concept of allostery in which macromolecules switch between two different conformations is a central theme in biological processes ranging from gene regulation to cell signaling to enzymology. Allosteric enzymes pervade metabolic…
Colloidal model systems allow studying crystallization kinetics under fairly ideal conditions with rather well characterized pair interactions and minimized external influences. In complementary approaches therefore experiment, analytic…
A geometrical model which captures the main ingredients governing atom-diatom collinear chemical reactions is proposed. This model is neither near-integrable nor hyperbolic, yet it is amenable to analysis using a combination of the recently…
We offer the parameter, interpreted as the "chemical potential", which is sensitive to the first order phase transition: it must decrease with number of evaporating (produced) particles (hadrons) if the (interacting hadron or/and QCD…
The aim of this work is to address issues where formal specifications cannot be realized on a given dynamical system subjected to a changing environment. Such failures occur whenever the dynamics of the system restrict the robot in such a…
Coalescing ballistic annihilation is an interacting particle system intended to model features of certain chemical reactions. Particles are placed with independent and identically distributed spacings on the real line and begin moving with…
Mathematical models are increasingly being used to understand complex biochemical systems, to analyze experimental data and make predictions about unobserved quantities. However, we rarely know how robust our conclusions are with respect to…
Single enzyme chemotaxis is a phenomenon by which a non-equilibrium spatial distribution of an enzyme is created and maintained by concentration gradients of the substrate and product of the catalyzed reaction. These gradients can arise…
We distinguish a mechanical representation of the world in terms of point masses with positions and momenta and the chemical representation of the world in terms of populations of different individuals, each with intrinsic stochasticity,…
Processes controlled by stochastic synthesis and degradation (SSD) are widespread in biology but their reaction kinetics are not well understood. Using methods borrowed from the theory of resetting processes, we determine the first-passage…
Motor enzymes catalyze chemical reactions, like the hydrolysis of ATP, and in the process they also perform work. Recent studies indicate that motor enzymes perform work with specific intermediate steps in their catalyzed reactions,…