Oscillation dynamic mechanism driven by time delays in the competent gene regulatory circuit of B. subtilis

Bacillus subtilis with competent states absorbs DNA and may improve the growth of bacteria by integrating new genetic material. Therefore, it is important to clarify how the genes interact in the circuit so that cells enter into a competent state or return to a vegetative state. The gene regulatory circuit consists of two positive feedback loops and one negative feedback loop. In this paper, a mathematical model is developed by considering transcription time delays to further study dynamic behavior of the B. subtilis competent gene regulatory network. Combined with theoretical calculation and numerical simulation, it is verified that the time delay in indirect transcription inhibition indeed has the effect of inducing the periodic oscillation of the B. subtilis competent system. In addition, some important chemical reaction rates can also regulate system dynamic behavior. However, under the control of time delay, the effects of the important chemical reaction rates have changed significantly. In particular, the time delay can advance critical value of the important chemical reaction rates where vibration occurs and can also weaken or even eliminate the effect of the important chemical reaction rates. These results will help us to analyze the competent state of B. subtilis.

The effects of gravitational potential on chemical reaction rates

This study aims to answer through a mathematical model and its numerical simulation the question whether the kinetic rate constants of chemical reactions are influenced by the strength of gravitational field. In order to calculate the effects of gravity on the kinetic rate constants, the model of kinetic rate constants derived from collision theory is amended by introducing the mass and length corrections provided by general relativity. Numerical simulations of the model show that the rate constant is higher where the gravitational field is more intense.

Partitioning Entropy with Action Mechanics: Predicting Chemical Reaction Rates and Gaseous Equilibria of Reactions of Hydrogen from Molecular Properties

Our intention is to provide easy methods for estimating entropy and chemical potentials for gas phase reactions. Clausius’ virial theorem set a basis for relating kinetic energy in a body of independent material particles to its potential energy, pointing to their complementary role with respect to the second law of maximum entropy. Based on this partitioning of thermal energy as sensible heat and also as a latent heat or field potential energy, in action mechanics we express the entropy of ideal gases as a capacity factor for enthalpy plus the configurational work to sustain the relative translational, rotational, and vibrational action. This yields algorithms for estimating chemical reaction rates and positions of equilibrium. All properties of state including entropy, work potential as Helmholtz and Gibbs energies, and activated transition state reaction rates can be estimated, using easily accessible molecular properties, such as atomic weights, bond lengths, moments of inertia, and vibrational frequencies. We conclude that the large molecular size of many enzymes may catalyze reaction rates because of their large radial inertia as colloidal particles, maximising action states by impulsive collisions. Understanding how Clausius’ virial theorem justifies partitioning between thermal and statistical properties of entropy, yielding a more complete view of the second law’s evolutionary nature and the principle of maximum entropy. The ease of performing these operations is illustrated with three important chemical gas phase reactions: the reversible dissociation of hydrogen molecules, lysis of water to hydrogen and oxygen, and the reversible formation of ammonia from nitrogen and hydrogen. Employing the ergal also introduced by Clausius to define the reversible internal work overcoming molecular interactions plus the configurational work of change in Gibbs energy, often neglected; this may provide a practical guide for managing industrial processes and risk in climate change at the global scale. The concepts developed should also have value as novel methods for the instruction of senior students.

Partitioning Entropy with Action Mechanics: Predicting Chemical Reaction Rates and Gaseous Equilibria of Reactions of Hydrogen from Molecular Properties

Clausius’ virial theorem set a basis for relating kinetic energy in a body of independent material particles to its potential energy, pointing to their complementary role with respect to the second law of maximum entropy. In action mechanics, expressing the entropy of ideal gases as a capacity factor for sensible heat or enthalpy plus the configurational work to sustain the relative translational, rotational and vibrational action yields algorithms for estimating chemical reaction rates and positions of equilibrium. All properties of state including entropy, work potential as Helmholtz and Gibbs energies and activated transition state reaction rates can be estimated, using easily accessible molecular properties, such as atomic weights, bond lengths, moments of inertia and vibrational frequencies. Understanding how Clausius’ virial theorem balances the internal kinetic energy with field potential energy justifies partitioning between thermal and statistical properties of entropy, yielding a more complete view of the evolutionary nature of the second law of thermodynamics. The ease of performing these operations is illustrated by three important chemical gas phase reactions, the reversible dissociation of the hydrogen molecules, lysis of water to hydrogen and oxygen and the reversible formation of ammonia from nitrogen and hydrogen. Employing the ergal also introduced by Clausius to define the reversible internal work to overcome molecular interactions plus the configurational internal work of negative Gibbs energy as a function of volume or pressure may provide a practical guide for managing risk in industrial processes and climate change at the global scale.

A general model for temperature-dependence in biology

Temperature affects all biological rates and has far reaching consequences from bioengineering [1] to predicting ecological shifts under a changing climate [2-3], and more recently, to pandemic spread [4]. Temperature response in biological systems is characteristically asymmetric and nonlinear, with an exponential phase of increase followed by a concave up-ward or downward phase [5]. Current models for quantitatively describing the temperature response include simple but empirical equations (such as Arrhenius’) or models derived from first principles which are often overly complicated (i.e. with many parameters). Moreover, their theoretical framework does not include how parameters vary, nor their applicability across multiple scales and taxa, or whether they exhibit universality [1-7]. Here, we derive a new mechanistic, yet simple, model for the temperature dependence of biological rates based on the Eyring-Evans-Polanyi theory governing chemical reaction rates, which is applicable across all scales from the micro to the macro. Assuming only that the conformational entropy of molecules changes with temperature, we derive a model for the temperature dependence which takes the form of an exponential function modified by a power-law. Data for a wide variety of biological rates from molecular to ecological scales and across multiple taxonomic groups agree well with our predictions. Furthermore, our framework predicts values for the thermodynamic parameters, and leads to a single parameterless universal scaling curve on which data across all scales and taxa collapse.

Resonant collisional shielding of reactive molecules using electric fields

Full control of molecular interactions, including reactive losses, would open new frontiers in quantum science. We demonstrate extreme tunability of ultracold chemical reaction rates by inducing resonant dipolar interactions by means of an external electric field. We prepared fermionic potassium-rubidium molecules in their first excited rotational state and observed a modulation of the chemical reaction rate by three orders of magnitude as we tuned the electric field strength by a few percent across resonance. In a quasi–two-dimensional geometry, we accurately determined the contributions from the three dominant angular momentum projections of the collisions. Using the resonant features, we shielded the molecules from loss and suppressed the reaction rate by an order of magnitude below the background value, thereby realizing a long-lived sample of polar molecules in large electric fields.