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Intracellular transport is an essential function in eucaryotic cells, facilitated by motor proteins - proteins converting chemical energy into kinetic energy. It is known that motor proteins work in teams enabling unidirectional and…
Ion transport in biological tissues is crucial in the study of many biological and pathological problems. Some multi-cellular structures, like smooth muscles on the vessel walls, could be treated as periodic bi-domain structures, which…
We introduce and theoretically investigate a minimal particle-based model for a new class of active matter where particles exhibit directional, volume-conserving division in confinement while interacting sterically, mimicking cells in early…
Diffusive transport of particles or, more generally, small objects is a ubiquitous feature of physical and chemical reaction systems. In configurations containing confining walls or constrictions transport is controlled both by the…
A cellular bleb grows when a portion of the cell membrane detaches from the underlying cortex under the influence of a cytoplasmic pressure. We develop a quantitative model for the growth and dynamics of these objects in a simple…
Many cell functions are accomplished thanks to intracellular transport mechanisms of macromolecules along filaments. Molecular motors such as dynein or kinesin are proteins playing a primary role in these processes. The behavior of such…
The transport of self-propelled particles such as bacteria and phoretic swimmers through crowded heterogeneous environments is relevant to many natural and engineering processes, from biofilm formation and contamination processes to…
Dynamic properties of molecular motors that fuel their motion by actively interacting with underlying molecular tracks are studied theoretically via discrete-state stochastic ``burnt-bridge'' models. The transport of the particles is viewed…
Many cellular processes require a polarization axis which generally initially emerges as an inhomogeneous distribution of molecular markers in the cell. We present a simple analytical model of a general mechanism of cell polarization taking…
Collective transport through channels shows surprising properties under one-dimensional confinement: particles in a single file exhibit sub-diffusive behavior, while liquid confinement causes distance-independent correlations between the…
We study the classical and quantum transport processes on some finite networks and model them by continuous-time random walks (CTRW) and continuous-time quantum walks (CTQW), respectively. We calculate the classical and quantum transition…
In living cells, molecular motors create activity that enhances the diffusion of particles throughout the cytoplasm, and not just ones attached to the motors. We demonstrate initial steps toward creating artificial cells that mimic this…
Modeling of ion transport via plasma membrane needs identification and quantitative understanding of the involved processes. Brief characterization of main ion transport systems of a yeast cell (Pma1, Ena1, TOK1, Nha1, Trk1, Trk2,…
Information delivery via molecular signals is abundant in nature and potentially useful for industry sensing. Many propagation channels (e.g., tissue membranes and catalyst beds) contain porous medium materials and the impact this has on…
In this paper a lattice model for the diffusional transport of particles in the interphase cell nucleus is proposed. The dynamic behaviour of single chains on the lattice is investigated and Rouse scaling is verified. Dynamical dense…
We theoretically investigate how information flows when two particles interact with each other. Understanding the physical mechanisms of directional information flow is crucial for advancing information thermodynamics and stochastic…
The transport of individual entities through interconnected structures is a process of practical relevance both in biology and technology. Examples are given by diffusive dynamics of molecules in porous structures. In soft environments,…
Modeling and simulation are transforming all fields of biology. Tools like AlphaFold have revolutionized structural biology, while molecular dynamics simulations provide invaluable insights into the behavior of macromolecules in solution or…
One common feature of a vehicle, an ant and a kinesin motor is that they all convert chemical energy, derived from fuel or food, into mechanical energy required for their forward movement; such objects have been modelled in recent years as…
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…