This chapter deals with correlation and response functions in equilibrium and in nonequilibrium steady states for a Langevin dynamics. First, the harmonic oscillator in equilibrium is discussed as a paradigmatic case. In the general nonlinear case, it is shown how time-derivatives in correlation functions can be replaced by state variables. The response function is derived within the path integral formalism. It can be expressed by various forms of a correlation function. One particularly transparent version restores the form of the equilibrium fluctuation-dissipation theorem for a nonequilibrium steady state. A second strategy to derive a response function starts with the perturbed Fokker–Plank operator. Causality imposes the Kramers–Kronig relations between the real and imaginary parts of the response function. Through the Harada–Sasa relation, the deviation from the equilibrium form of the fluctuation-dissipation relation can be related to the mean entropy production.

In this chapter, we explore theoretical aspects of the origin of life problem. Firstly, we address the Chicken and Egg problem referring to the “RNA world.” We explain a mathematical model of the RNA replication system introduced by Eigen and discuss the conditions necessary for self-replication, referring “error catastrophe.” As a potential solution, we discuss the “hypercycle,” alongside its vulnerabilities and the acquisition of evolvability through compartmentalization. On another front, we examine Dyson’s catalytic reaction system as an alternative hypothesis, showing that catalytic reaction networks capable of maintaining themselves and undergoing imperfect reproduction may have appeared first. We also refer to a simple model of polymer reactions, arguing that such autocatalytic reaction networks can stochastically emerge, as proposed by Kauffman. Furthermore, we describe a cell model featuring an intracellular chemical reaction network that divides based on its state, highlighting the universal nature of reaction dynamics in replicating cells and the power-law distribution of chemical abundance (Zipf’s law), which has been verified across many organisms. Additionally, we introduce the concept of “minority control” in catalytic reaction networks, which can carry primitive genetic information. Finally, we discuss perspectives on research regarding the origin of life.

This chapter serves as an intuitive introduction to dynamical systems within the realm of biological systems, through visual representations of state space dynamics. Biological examples and experimental realizations are described to demonstrate how dynamical systems concepts are applicable in solving fundamental problems in cell biology. Differential equations are taken as typical of dynamical systems, and we explain topics such as nullcline and fixed points, linear stability analysis, and attractors, elucidating their significance using systems such as gene toggle switches. The introduction of limit cycles and the Poincaré–Bendixson theorem in two-dimensional systems is followed by examples such as the Brusselator and the repressilator system. Furthermore, we explore the basin structure in multi-attractor systems and provide detailed explanations using toggle switch systems to illustrate time-scale separation between variables and adiabatic elimination of variables. Several instances of co-dimension 1 bifurcations commonly observed in biological systems are presented, with a discussion of their biological significance in processes like cell differentiation. Finally, chaos theory is introduced.

For the Brownian motion of a particle in a fluid, the Langevin equation for its momentum is introduced phenomenologically. The strength of the noise is shown to be related to friction, and, in a second step, to the diffusion coefficient. Excellent agreement with experiments on a levitated particle in gas is demonstrated. This phenomenological Langevin equation is then shown to follow from a general projection approach to the underlying Hamiltonian dynamics of the full system in the limit of an infinite mass ratio between Brownian particles and fluid molecules. For Brownian motion in liquids, additional time-scales enter that are discussed phenomenologically and illustrated with experiments.

There are two great post-Newtonian steps in classical mechanics. The first is the Lagrangian formulation and the accompanying principle of least action. The second is the Hamiltonian formulation, which is yet another way of writing Newtons equation of motion that uncovers what is really going on. This is where we start to see the deep and beautiful mathematical structure that underlies classical mechanics. It is also where we can make connections to what comes next, with quantum mechanics following very naturally from the Hamiltonian formulation.

If youre going to understand one thing in physics then it should be the harmonic oscillator. It is simple system that underlies nearly everything else that we do. This chapter studies the quantum harmonic oscillator, solving it several times in different ways to highlight different features.

The canonical description of an aqueous solution with an embedded enzyme is introduced. The mesostates of this enzyme comprise different conformations which are affected by binding and release of solute molecules. Thermodynamic potentials of these mesostates are identified. Heat and entropy production associated with transitions between these mesostates are determined both for a simple toy model and in the general case.

Our discussion in early chapters captures the spirit of quantum mechanics but is restricted to particles moving along a line. Thats not very unrealistic. In this chapter we breathe some life into quantum particles and allow them to roam in three-dimensional space. This entails an understanding of angular momentum. We will pay particular attention to the hydrogen atom, whose quantum solution was one of the first great triumphs of quantum mechanics and still underlies all of atomic physics.

The two body problem is the question of how two objects – say the Sun and the Earth – move under their mutual gravitational attraction. The problem is, happily, fully solvable and the purpose of this chapter is to fully solve it. We will understand how Keplers laws of planetary motion arise from the more fundamental Newtonian law of gravity. Because the electrostatic force has exactly the same form as the force of gravity, we can also use our solutions to understand how electrons scatter off atoms, a famous experiment performed by Rutherford that led to an understanding of the structure of matter.

For a system in contact with a heat bath, it is shown how the distribution of any observable follows from a microcanonical description for the isolated system consisting of the system of interest and heat bath. The weak coupling approximation then leads to the standard expression for the canonical distribution. Free energy, canonical entropy, and pressure are introduced. For large systems, the equivalence of this canonical description with the microcanonical one is shown. For systems in contact with a particle reservoir, the grand-canonical distribution is derived. If the weak coupling approximation does not hold, the corrections due to strong coupling are determined. In particular, internal energy, free energy ,and entropy are identified such that the usual relations for these thermodynamic potentials hold true even in strong coupling.