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Lipid membranes have complex compositions and modeling the thermodynamic properties of multi-component lipid systems remains a remote goal. In this work we attempt to describe the thermodynamics of binary lipid mixtures by mapping…
The issue of the thermodynamics of a system of distinguishable particles is discussed in this paper. In constructing the statistical mechanics of distinguishable particles from the definition of Boltzmann entropy, it is found that the…
The proper definition of entropy is fundamental to the relationship between statistical mechanics and thermodynamics. It also plays a major role in the recent debate about the validity of the concept of negative temperature. In this paper,…
Thermodynamics makes definite predictions about the thermal behavior of macroscopic systems in and out of equilibrium. Statistical mechanics aims to derive this behavior from the dynamics and statistics of the atoms and molecules making up…
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…
Molecular simulations can provide microscopic insight into the physical and chemical driving forces of complex molecular processes. Despite continued advancement of simulation methodology, model errors may lead to inconsistencies between…
Mechanistic growth models play a major role in bioprocess engineering, design, and control. Their reasonable predictive power and their high level of interpretability make them an essential tool for computer aided engineering methods.…
The purpose of the dynamics of moving systems is to search for the mathematical model that describes the link between the resultant applied force, that is the cause, and the speed of system that is the effect. This mathematical link…
Active matter is rapidly becoming a key paradigm of out-of-equilibrium soft matter exhibiting complex collective phenomena, yet the thermodynamics of such systems remain poorly understood. In this letter we study the nonequilbrium…
Biological forces govern essential cellular and molecular processes in all living organisms. Many cellular forces, e.g. those generated in cyclic conformational changes of biological machines, have repetitive components. However, little is…
We present a new kinetic equation for cell migration driven by mechanical interactions with the substrate, an effect not previously captured in kinetic models, and essential for explaining observed collective behaviors such as those in…
Binary fluid mixtures are examples of complex fluids whose microstructure and flow are strongly coupled. For pairs of simple fluids, the microstructure consists of droplets or bicontinuous demixed domains and the physics is controlled by…
The interplay between cytoskeletal architecture and the nonlinearity of the interactions due to bucklable filaments plays a key role in modulating the cell's mechanical stability and affecting its structural rearrangements. We study a model…
We study an ideal-gas-like model where the particles exchange energy stochastically, through energy conserving scattering processes, which take place if and only if at least one of the two particles has energy below a certain energy…
We show that active transport processes in biological systems can be understood through a local equilibrium description formulated at the mesoscale, the scale to describe stochastic processes. This new approach uses the method established…
Cells move by run and tumble, a kind of dynamics in which the cell alternates runs over straight lines and re-orientations. This erratic motion may be influenced by external factors, like chemicals, nutrients, the extra-cellular matrix, in…
We study a model of synthetic molecular motor - a [3]-catenane consisting of two small macrocycles mechanically interlocked with a bigger one - subjected to a time-dependent driving using stochastic thermodynamics. The model presents…
While mechanobiology has demonstrated that precise control over mechanical properties at the whole-cell level is crucial for many biological functions, comparatively little attention has been paid to the intracellular mechanical properties.…
While many good textbooks are available on Protein Structure, Molecular Simulations, Thermodynamics and Bioinformatics methods in general, there is no good introductory level book for the field of Structural Bioinformatics. This book aims…
Mechanically induced folding of passive cross-linkers is a fundamental biological phenomenon. A typical example is a conformational change in myosin II responsible for the power-stroke in skeletal muscles. In this paper we present an…