Related papers: A Fully Anisotropic Formulation of Stochastic Cell…

Molecular dynamics simulations require barostats to be performed at constant pressure. The usual recipe is to employ the Berendsen barostat first, which displays a first-order volume relaxation efficient in equilibration but results in…

We analyse the effect of intrinsic fluctuations on the properties of bistable stochastic systems with time scale separation operating under1 quasi-steady state conditions. We first formulate a stochastic generalisation of the quasi-steady…

The authors present a new molecular dynamics algorithm for sampling the isothermal-isobaric ensemble. In this approach the velocities of all particles and volume degrees of freedom are rescaled by a properly chosen random factor. The…

We present a method for enhanced sampling of molecular dynamics simulations using stochastic resetting. Various phenomena, ranging from crystal nucleation to protein folding, occur on timescales that are unreachable in standard simulations.…

Molecular dynamics simulations are widely used across chemistry, physics, and biology, providing quantitative insight into complex processes with atomic detail. However, their limited timescale of a few microseconds is a significant…

The dynamics of cellular pattern formation is crucial for understanding embryonic development and tissue morphogenesis. Recent studies have shown that human dermal fibroblasts cultured on liquid crystal elastomers can exhibit an increase in…

Molecular dynamics is one of the most commonly used approaches for studying the dynamics and statistical distributions of many physical, chemical, and biological systems using atomistic or coarse-grained models. It is often the case,…

A stochastic procedure is developed which allows one to express Pontryagin's maximum principle for dissipative quantum system solely in terms of stochastic wave functions. Time-optimal controls can be efficiently computed without computing…

Stochastic processes govern the time evolution of a huge variety of realistic systems throughout the sciences. A minimal description of noisy many-particle systems within a Markovian picture and with a notion of spatial dimension is given…

A ubiquitous feature of living cells is their growth over time followed by division into daughter cells. How isogenic cell populations maintain size homeostasis, i.e., a narrow distribution of cell size, is an intriguing fundamental…

Cell proliferation and cell movement are fundamentally stochastic processes which lead to variability in the growth and spatial structure of cell populations in many biological settings, such as cell invasion, wound healing, and tumour…

We have developed a coarse-grained formulation for modeling the dynamic behavior of cells quantitatively, based on stochasticity and heterogeneity, rather than on biochemical reactions. We treat each reaction as a continuous-time stochastic…

A formalism is developed which describes the extent to which stochastic oscillations in biochemical models are synchronised. It is based on the calculation of the complex coherence function within the linear noise approximation. The method…

Classic models of cell size control consider cells divide while reaching a threshold, e.g. size, age, or size extension. The molecular basis of the threshold involves multiple layers of regulation as well as gene noises. In this work, we…

Molecular dynamics is often considered as a numerical experiment. The error bars on the results are therefore mandatory, but sometimes difficult to determine and computationally demanding. As a low-cost approach, we describe the application…

The proper functioning of multicellular organisms requires the robust establishment of precise proportions between distinct cell-types. This developmental differentiation process typically involves intracellular regulatory and stochastic…

Cell size control and homeostasis is a major topic in cell biology yet to be fully understood. Several growth laws like the timer, adder, and sizer were proposed, and mathematical approaches that model cell growth and division were…

We present a theory for the number fluctuations of a quasi-two-dimensional (quasi-2D) dipolar Bose-Einstein condensate measured with finite resolution cells. We show that when the dipoles are tilted to have a component parallel to the plane…

Investigation of protein self-assembly processes is important for the understanding of the growth processes of functional proteins as well as disease-causing amyloids. Inside cells, intrinsic molecular fluctuations are so high that they…

Because most chemical or biological experiments are performed under conditions of controlled pressure and temperature, it is important to simulate the isobaric-isothermal ensemble at the atomic level to reveal the microscopic mechanism. By…