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In cells and in vitro assays the number of motor proteins involved in biological transport processes is far from being unlimited. The cytoskeletal binding sites are in contact with the same finite reservoir of motors (either the cytosol or…
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…
Machine learning techniques including neural networks are popular tools for materials and chemical scientists with applications that may provide viable alternative methods in the analysis of structure and energetics of systems ranging from…
Modeling biological processes is a highly demanding task because not all processes are fully understood. Mathematical models allow us to test hypotheses about possible mechanisms of biological processes. The mathematical mechanisms…
Dynamic properties of molecular motors whose motion is powered by interactions with specific lattice bonds are studied theoretically with the help of discrete-state stochastic "burnt-bridge" models. Molecular motors are depicted as random…
Transport of molecular motors along protein filaments in a half-closed geometry is a common feature of biologically relevant processes in cellular protrusions. Using a lattice gas model we study how the interplay between active and…
Intracellular transport along microtubules or actin filaments, powered by molecular motors such as kinesins, dyneins or myosins, has been recently modeled using one-dimensional driven lattice gases. We discuss some generalizations of these…
Biological molecular machines convert free energy between different forms in cells, often at high efficiency. Optimal control theory provides a framework to elucidate design principles governing energetically efficient driving. Here, we use…
We present a machine learning framework for modeling protein dynamics. Our approach uses L1-regularized, reversible hidden Markov models to understand large protein datasets generated via molecular dynamics simulations. Our model is…
The effect of sequence heterogeneity on the dynamics of molecular motors is reviewed and analyzed using a set of recently introduced lattice models. First, we review results for the influence of heterogenous tracks such as a single-strand…
In this paper we investigate the use of path-integral formalism and the concepts of entropy and traffic in the context of molecular motors. We show that together with time-reversal symmetry breaking arguments one can find bounds on…
Molecular machines consist of either a single protein or a macromolecular complex composed of protein and RNA molecules. Just like their macroscopic counterparts, each of these nano-machines has an engine that "transduces" input energy into…
We theoretically study the transport properties of self-propelled particles on complex structures, such as motor proteins on filament networks. A general master equation formalism is developed to investigate the persistent motion of…
The molecular motor protein kinesin plays a key role in fundamental cellular processes such as intracellular transport, mitotic spindle formation, and cytokinesis, with important implications for neurodegenerative and cancer disease…
Unraveling the dynamical motions of biomolecules is essential for bridging their structure and function, yet it remains a major computational challenge. Molecular dynamics (MD) simulation provides a detailed depiction of biomolecular…
This study employed an artificial intelligence-enhanced molecular simulation framework to enable efficient Path Integral Molecular Dynamics (PIMD) simulations. Owing to its modular architecture and high-throughput capabilities, the…
Inspired by patterns observed in mixtures of microtubules and molecular motors, we propose continuum equations for the evolution of motor density, and microtubule orientation. The chief ingredients are the transport of motors along tubules,…
Many biological functions are executed by molecular machines, which consume energy and convert it into mechanical work. Biological machines have evolved to transport cargo, facilitate folding of proteins and RNA, remodel chromatin and…
Many different types of cellular cargos are transported bidirectionally along microtubules by teams of molecular motors. The motion of this cargo-motors system has been experimentally characterized in vivo as processive with rather…
We examine the dependence of the physical quantities of the rotatory molecular motor, such as the rotation velocity and the proton translocation rate, on the chemical reaction rate using the model based only on diffusion process. A peculiar…